Integrated Reconfigurable Intelligent Systems (IRIS) for Complex Naval Systems

DTIC Science & Technology

2009-12-31

written. The new implementation supports the XML dialect called dashML. The plug-in is written in Java script using a flexible extension of the...human in the loop control was improved and documented, and the script for integration was developed; further study on theoretical framework for...reference damage controller was developed and tested; the model of human in the loop control was improved and documented, and the script for integrating

Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF)

PubMed Central

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L.; Sanders, Brian; Grethe, Jeffrey S.; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W.; Martone, Maryann E.

2009-01-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov. PMID:18958629

Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF).

PubMed

Gupta, Amarnath; Bug, William; Marenco, Luis; Qian, Xufei; Condit, Christopher; Rangarajan, Arun; Müller, Hans Michael; Miller, Perry L; Sanders, Brian; Grethe, Jeffrey S; Astakhov, Vadim; Shepherd, Gordon; Sternberg, Paul W; Martone, Maryann E

2008-09-01

The overarching goal of the NIF (Neuroscience Information Framework) project is to be a one-stop-shop for Neuroscience. This paper provides a technical overview of how the system is designed. The technical goal of the first version of the NIF system was to develop an information system that a neuroscientist can use to locate relevant information from a wide variety of information sources by simple keyword queries. Although the user would provide only keywords to retrieve information, the NIF system is designed to treat them as concepts whose meanings are interpreted by the system. Thus, a search for term should find a record containing synonyms of the term. The system is targeted to find information from web pages, publications, databases, web sites built upon databases, XML documents and any other modality in which such information may be published. We have designed a system to achieve this functionality. A central element in the system is an ontology called NIFSTD (for NIF Standard) constructed by amalgamating a number of known and newly developed ontologies. NIFSTD is used by our ontology management module, called OntoQuest to perform ontology-based search over data sources. The NIF architecture currently provides three different mechanisms for searching heterogeneous data sources including relational databases, web sites, XML documents and full text of publications. Version 1.0 of the NIF system is currently in beta test and may be accessed through http://nif.nih.gov.

Information Retrieval System for Japanese Standard Disease-Code Master Using XML Web Service

PubMed Central

Hatano, Kenji; Ohe, Kazuhiko

2003-01-01

Information retrieval system of Japanese Standard Disease-Code Master Using XML Web Service is developed. XML Web Service is a new distributed processing system by standard internet technologies. With seamless remote method invocation of XML Web Service, users are able to get the latest disease code master information from their rich desktop applications or internet web sites, which refer to this service. PMID:14728364

Automated software system for checking the structure and format of ACM SIG documents

NASA Astrophysics Data System (ADS)

Mirza, Arsalan Rahman; Sah, Melike

2017-04-01

Microsoft (MS) Office Word is one of the most commonly used software tools for creating documents. MS Word 2007 and above uses XML to represent the structure of MS Word documents. Metadata about the documents are automatically created using Office Open XML (OOXML) syntax. We develop a new framework, which is called ADFCS (Automated Document Format Checking System) that takes the advantage of the OOXML metadata, in order to extract semantic information from MS Office Word documents. In particular, we develop a new ontology for Association for Computing Machinery (ACM) Special Interested Group (SIG) documents for representing the structure and format of these documents by using OWL (Web Ontology Language). Then, the metadata is extracted automatically in RDF (Resource Description Framework) according to this ontology using the developed software. Finally, we generate extensive rules in order to infer whether the documents are formatted according to ACM SIG standards. This paper, introduces ACM SIG ontology, metadata extraction process, inference engine, ADFCS online user interface, system evaluation and user study evaluations.

A comparison of database systems for XML-type data.

PubMed

Risse, Judith E; Leunissen, Jack A M

2010-01-01

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

XML Flight/Ground Data Dictionary Management

NASA Technical Reports Server (NTRS)

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 Style Guide

DTIC Science & Technology

2015-07-01

Acronyms ASCII American Standard Code for Information Interchange DAU data acquisition unit DDML data display markup language IHAL...Transfer Standard URI uniform resource identifier W3C World Wide Web Consortium XML extensible markup language XSD XML schema definition XML Style...Style Guide, RCC 125-15, July 2015 1 Introduction The next generation of telemetry systems will rely heavily on extensible markup language (XML

An XML Data Model for Inverted Image Indexing

NASA Astrophysics Data System (ADS)

So, Simon W.; Leung, Clement H. C.; Tse, Philip K. C.

2003-01-01

The Internet world makes increasing use of XML-based technologies. In multimedia data indexing and retrieval, the MPEG-7 standard for Multimedia Description Scheme is specified using XML. The flexibility of XML allows users to define other markup semantics for special contexts, construct data-centric XML documents, exchange standardized data between computer systems, and present data in different applications. In this paper, the Inverted Image Indexing paradigm is presented and modeled using XML Schema.

A Survey in Indexing and Searching XML Documents.

ERIC Educational Resources Information Center

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…

XML in Libraries.

ERIC Educational Resources Information Center

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…

Adaptive Hypermedia Educational System Based on XML Technologies.

ERIC Educational Resources Information Center

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…

XWeB: The XML Warehouse Benchmark

NASA Astrophysics Data System (ADS)

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.

Setting the Standard: XML on Campus.

ERIC Educational Resources Information Center

Rawlins, Mike

2001-01-01

Explains what XML (Extensible Markup Language) is; where to find it in a few years (everywhere from Web pages, to database management systems, to common campus applications); issues that will make XML somewhat of an experimental strategy in the near term; and the importance of decision-makers being abreast of XML trends in standards, tools…

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

DTIC Science & Technology

2003-03-01

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

Framework and prototype for a secure XML-based electronic health records system.

PubMed

Steele, Robert; Gardner, William; Chandra, Darius; Dillon, Tharam S

2007-01-01

Security of personal medical information has always been a challenge for the advancement of Electronic Health Records (EHRs) initiatives. eXtensible Markup Language (XML), is rapidly becoming the key standard for data representation and transportation. The widespread use of XML and the prospect of its use in the Electronic Health (e-health) domain highlights the need for flexible access control models for XML data and documents. This paper presents a declarative access control model for XML data repositories that utilises an expressive XML role control model. The operational semantics of this model are illustrated by Xplorer, a user interface generation engine which supports search-browse-navigate activities on XML repositories.

James Webb Space Telescope XML Database: From the Beginning to Today

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Fatig, Curtis C.

2005-01-01

The James Webb Space Telescope (JWST) Project has been defining, developing, and exercising the use of a common eXtensible Markup Language (XML) for the command and telemetry (C&T) database structure. JWST is the first large NASA space mission to use XML for databases. The JWST project started developing the concepts for the C&T database in 2002. The database will need to last at least 20 years since it will be used beginning with flight software development, continuing through Observatory integration and test (I&T) and through operations. Also, a database tool kit has been provided to the 18 various flight software development laboratories located in the United States, Europe, and Canada that allows the local users to create their own databases. Recently the JWST Project has been working with the Jet Propulsion Laboratory (JPL) and Object Management Group (OMG) XML Telemetry and Command Exchange (XTCE) personnel to provide all the information needed by JWST and JPL for exchanging database information using a XML standard structure. The lack of standardization requires custom ingest scripts for each ground system segment, increasing the cost of the total system. Providing a non-proprietary standard of the telemetry and command database definition formation will allow dissimilar systems to communicate without the need for expensive mission specific database tools and testing of the systems after the database translation. The various ground system components that would benefit from a standardized database are the telemetry and command systems, archives, simulators, and trending tools. JWST has exchanged the XML database with the Eclipse, EPOCH, ASIST ground systems, Portable spacecraft simulator (PSS), a front-end system, and Integrated Trending and Plotting System (ITPS) successfully. This paper will discuss how JWST decided to use XML, the barriers to a new concept, experiences utilizing the XML structure, exchanging databases with other users, and issues that have been experienced in creating databases for the C&T system.

Verified OS Interface Code Synthesis

DTIC Science & Technology

2016-12-01

in this case we are using the ARMv7 processor architecture ). The application accomplishes this task by issuing the swi (“software interrupt...manual version 4.0.0) on the ARM architecture . To alleviate this problem,we developed an XML-based domain specific language (DSL) in which each...Untyped Retype Table 2.1: seL4 Architecture Independent System Calls. of r2, r3, r4 and r5 into the message registers of the thread’s IPC buffer and

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

ERIC Educational Resources Information Center

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…

Interoperability, Data Control and Battlespace Visualization using XML, XSLT and X3D

DTIC Science & Technology

2003-09-01

26 Rosenthal, Arnon, Seligman , Len and Costello, Roger, XML, Databases, and Interoperability, Federal Database Colloquium, AFCEA, San Diego...79 Rosenthal, Arnon, Seligman , Len and Costello, Roger, “XML, Databases, and Interoperability”, Federal Database Colloquium, AFCEA, San Diego, 1999... Linda , Mastering XML, Premium Edition, SYBEX, 2001 Wooldridge, Michael , An Introduction to MultiAgent Systems, Wiley, 2002 PAPERS Abernathy, M

EOS ODL Metadata On-line Viewer

NASA Astrophysics Data System (ADS)

Yang, J.; Rabi, M.; Bane, B.; Ullman, R.

2002-12-01

We have recently developed and deployed an EOS ODL metadata on-line viewer. The EOS ODL metadata viewer is a web server that takes: 1) an EOS metadata file in Object Description Language (ODL), 2) parameters, such as which metadata to view and what style of display to use, and returns an HTML or XML document displaying the requested metadata in the requested style. This tool is developed to address widespread complaints by science community that the EOS Data and Information System (EOSDIS) metadata files in ODL are difficult to read by allowing users to upload and view an ODL metadata file in different styles using a web browser. Users have the selection to view all the metadata or part of the metadata, such as Collection metadata, Granule metadata, or Unsupported Metadata. Choices of display styles include 1) Web: a mouseable display with tabs and turn-down menus, 2) Outline: Formatted and colored text, suitable for printing, 3) Generic: Simple indented text, a direct representation of the underlying ODL metadata, and 4) None: No stylesheet is applied and the XML generated by the converter is returned directly. Not all display styles are implemented for all the metadata choices. For example, Web style is only implemented for Collection and Granule metadata groups with known attribute fields, but not for Unsupported, Other, and All metadata. The overall strategy of the ODL viewer is to transform an ODL metadata file to a viewable HTML in two steps. The first step is to convert the ODL metadata file to an XML using a Java-based parser/translator called ODL2XML. The second step is to transform the XML to an HTML using stylesheets. Both operations are done on the server side. This allows a lot of flexibility in the final result, and is very portable cross-platform. Perl CGI behind the Apache web server is used to run the Java ODL2XML, and then run the results through an XSLT processor. The EOS ODL viewer can be accessed from either a PC or a Mac using Internet Explorer 5.0+ or Netscape 4.7+.

δ-dependency for privacy-preserving XML data publishing.

PubMed

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, to demonstrate the proposed privacy scheme in practical application. Copyright © 2014. Published by Elsevier Inc.

Building VoiceXML-Based Applications

DTIC Science & Technology

2002-01-01

basketball games. The Busline systems were pri- y developed using an early implementation of VoiceXML he NBA Update Line was developed using VoiceXML...traveling in and out of Pittsburgh’s rsity neighborhood. The second project is the NBA Up- Line, which provides callers with real-time information NBA ... NBA UPDATE LINE The target user of this system is a fairly knowledgeable basket- ball fan; the system must therefore be able to provide detailed

Report of Official Foreign Travel to Montreal, Canada

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

Mason, J. D.

How can DOE, NNSA, and Y-12 best handle the integration of information from diverse sources, and what will best ensure that legacy data will survive changes in computing systems for the future? Although there is no simple answer, it is becoming increasingly clear throughout the information-management industry that a key component of both preservation and integration of information is the adoption of standardized data formats. The most notable standardized format is XML, to which almost all data is now migrating. XML is derived from SGML, as is HTML, the common language of the World Wide Web. XML is becoming increasinglymore » important as part of the Y-12 data infrastructure. Y-12 is implementing a new generation of XML-based publishing systems. Y-12 already has been supporting projects at DOE Headquarters, such as the Guidance Streamlining Initiative (GSI) that will result in the storage of classification guidance in XML. Y-12 collects some test data in XML as the result of Electronic Data Capture (EDC), and XML data is also used in Engineering Releases. I am participating in a series of projects sponsored by the PRIDE initiative that include the capture of dimensional certification and other similar records in XML, the creation of XML formats for Electronic Data Capture, and the creation of Quality Evaluation Reports in XML. In support of DOE's use of SGML, XML, HTML, Topic Maps, and related standards, I served 1985-2007 as chairman of the international committee responsible for SGML and standards derived from it, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations; I continue to belong to the committee. During the August 2010 trip, I co-chaired the conference Balisage 2010.« less

XML syntax for clinical laboratory procedure manuals.

PubMed

Saadawi, Gilan; Harrison, James H

2003-01-01

We have developed a document type description (DTD) in Extensable Markup Language (XML) 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 body of test information.

A distributed computing system for magnetic resonance imaging: Java-based processing and binding of XML.

PubMed

de Beer, R; Graveron-Demilly, D; Nastase, S; van Ormondt, D

2004-03-01

Recently we have developed a Java-based heterogeneous distributed computing system for the field of magnetic resonance imaging (MRI). It is a software system for embedding the various image reconstruction algorithms that we have created for handling MRI data sets with sparse sampling distributions. Since these data sets may result from multi-dimensional MRI measurements our system has to control the storage and manipulation of large amounts of data. In this paper we describe how we have employed the extensible markup language (XML) to realize this data handling in a highly structured way. To that end we have used Java packages, recently released by Sun Microsystems, to process XML documents and to compile pieces of XML code into Java classes. We have effectuated a flexible storage and manipulation approach for all kinds of data within the MRI system, such as data describing and containing multi-dimensional MRI measurements, data configuring image reconstruction methods and data representing and visualizing the various services of the system. We have found that the object-oriented approach, possible with the Java programming environment, combined with the XML technology is a convenient way of describing and handling various data streams in heterogeneous distributed computing systems.

XGI: a graphical interface for XQuery creation.

PubMed

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

2007-10-11

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

A Novel Navigation Paradigm for XML Repositories.

ERIC Educational Resources Information Center

Azagury, Alain; Factor, Michael E.; Maarek, Yoelle S.; Mandler, Benny

2002-01-01

Discusses data exchange over the Internet and describes the architecture and implementation of an XML document repository that promotes a navigation paradigm for XML documents based on content and context. Topics include information retrieval and semistructured documents; and file systems as information storage infrastructure, particularly XMLFS.…

ART-ML - a novel XML format for the biological procedures modeling and the representation of blood flow simulation.

PubMed

Karvounis, E C; Tsakanikas, V D; Fotiou, E; Fotiadis, D I

2010-01-01

The paper proposes a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of blood flow, mass transport and plaque formation, exported by ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in easy to handle 3D representations. The platform incorporates efficient algorithms which are able to perform blood flow simulation. In addition atherosclerotic plaque development is estimated taking into account morphological, flow and genetic factors. ART-ML provides a XML format that enables the representation and management of embedded models within the ARTool platform and the storage and interchange of well-defined information. This approach influences in the model creation, model exchange, model reuse and result evaluation.

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

In 2004, the Geography Markup Language (GML) Implementation Specification (version 3.1.1) was published by Open Geospatial Consortium, Inc. Now more and more applications in geospatial data sharing and interoperability depend on GML. The primary purpose of designing GML is for exchange and transportation of geo-information by standard modeling and encoding of geography phenomena. However, the problems of how to organize and access lots of GML data effectively arise in applications. The research on GML database focuses on these problems. The effective storage of GML data is a hot topic in GIS communities today. GML Database Management System (GDBMS) mainly deals with the problem of storage and management of GML data. Now two types of XML database, namely Native XML Database, and XML-Enabled Database are classified. Since GML is an application of the XML standard to geographic data, the XML database system can also be used for the management of GML. In this paper, we review the status of the art of XML database, including storage, index and query languages, management systems and so on, then move on to the GML database. At the end, the future prospect of GML database in GIS application is presented.

The Essen Learning Model--A Step towards a Representation of Learning Objectives.

ERIC Educational Resources Information Center

Bick, Markus; Pawlowski, Jan M.; Veith, Patrick

The importance of the Extensible Markup Language (XML) technology family in the field of Computer Assisted Learning (CAL) can not be denied. The Instructional Management Systems Project (IMS), for example, provides a learning resource XML binding specification. Considering this specification and other implementations using XML to represent…

Application of XML in DICOM

NASA Astrophysics Data System (ADS)

You, Xiaozhen; Yao, Zhihong

2005-04-01

As a standard of communication and storage for medical digital images, DICOM has been playing a very important role in integration of hospital information. In DICOM, tags are expressed by numbers, and only standard data elements can be shared by looking up Data Dictionary while private tags can not. As such, a DICOM file's readability and extensibility is limited. In addition, reading DICOM files needs special software. In our research, we introduced XML into DICOM, defining an XML-based DICOM special transfer format, XML-DCM, a DICOM storage format, X-DCM, as well as developing a program package to realize format interchange among DICOM, XML-DCM, and X-DCM. XML-DCM is based on the DICOM structure while replacing numeric tags with accessible XML character string tags. The merits are as following: a) every character string tag of XML-DCM has explicit meaning, so users can understand standard data elements and those private data elements easily without looking up the Data Dictionary. In this way, the readability and data sharing of DICOM files are greatly improved; b) According to requirements, users can set new character string tags with explicit meaning to their own system to extend the capacity of data elements; c) User can read the medical image and associated information conveniently through IE, ultimately enlarging the scope of data sharing. The application of storage format X-DCM will reduce data redundancy and save storage memory. The result of practical application shows that XML-DCM does favor integration and share of medical image data among different systems or devices.

XML technologies for the Omaha System: a data model, a Java tool and several case studies supporting home healthcare.

PubMed

Vittorini, Pierpaolo; Tarquinio, Antonietta; di Orio, Ferdinando

2009-03-01

The eXtensible markup language (XML) is a metalanguage which is useful to represent and exchange data between heterogeneous systems. XML may enable healthcare practitioners to document, monitor, evaluate, and archive medical information and services into distributed computer environments. Therefore, the most recent proposals on electronic health records (EHRs) are usually based on XML documents. Since none of the existing nomenclatures were specifically developed for use in automated clinical information systems, but were adapted to such use, numerous current EHRs are organized as a sequence of events, each represented through codes taken from international classification systems. In nursing, a hierarchically organized problem-solving approach is followed, which hardly couples with the sequential organization of such EHRs. Therefore, the paper presents an XML data model for the Omaha System taxonomy, which is one of the most important international nomenclatures used in the home healthcare nursing context. Such a data model represents the formal definition of EHRs specifically developed for nursing practice. Furthermore, the paper delineates a Java application prototype which is able to manage such documents, shows the possibility to transform such documents into readable web pages, and reports several case studies, one currently managed by the home care service of a Health Center in Central Italy.

XTCE GOVSAT Tool Suite 1.0

NASA Technical Reports Server (NTRS)

Rice, J. Kevin

2013-01-01

The XTCE GOVSAT software suite contains three tools: validation, search, and reporting. The Extensible Markup Language (XML) Telemetric and Command Exchange (XTCE) GOVSAT Tool Suite is written in Java for manipulating XTCE XML files. XTCE is a Consultative Committee for Space Data Systems (CCSDS) and Object Management Group (OMG) specification for describing the format and information in telemetry and command packet streams. These descriptions are files that are used to configure real-time telemetry and command systems for mission operations. XTCE s purpose is to exchange database information between different systems. XTCE GOVSAT consists of rules for narrowing the use of XTCE for missions. The Validation Tool is used to syntax check GOVSAT XML files. The Search Tool is used to search (i.e. command and telemetry mnemonics) the GOVSAT XML files and view the results. Finally, the Reporting Tool is used to create command and telemetry reports. These reports can be displayed or printed for use by the operations team.

A High-Availability, Distributed Hardware Control System Using Java

NASA Technical Reports Server (NTRS)

Niessner, Albert F.

2011-01-01

Two independent coronagraph experiments that require 24/7 availability with different optical layouts and different motion control requirements are commanded and controlled with the same Java software system executing on many geographically scattered computer systems interconnected via TCP/IP. High availability of a distributed system requires that the computers have a robust communication messaging system making the mix of TCP/IP (a robust transport), and XML (a robust message) a natural choice. XML also adds the configuration flexibility. Java then adds object-oriented paradigms, exception handling, heavily tested libraries, and many third party tools for implementation robustness. The result is a software system that provides users 24/7 access to two diverse experiments with XML files defining the differences

Cyberinfrastructure at IRIS: Challenges and Solutions Providing Integrated Data Access to EarthScope and Other Earth Science Data

NASA Astrophysics Data System (ADS)

Ahern, T. K.; Barga, R.; Casey, R.; Kamb, L.; Parastatidis, S.; Stromme, S.; Weertman, B. T.

2008-12-01

While mature methods of accessing seismic data from the IRIS DMC have existed for decades, the demands for improved interdisciplinary data integration call for new approaches. Talented software teams at the IRIS DMC, UNAVCO and the ICDP in Germany, have been developing web services for all EarthScope data including data from USArray, PBO and SAFOD. These web services are based upon SOAP and WSDL. The EarthScope Data Portal was the first external system to access data holdings from the IRIS DMC using Web Services. EarthScope will also draw more heavily upon products to aid in cross-disciplinary data reuse. A Product Management System called SPADE allows archive of and access to heterogeneous data products, presented as XML documents, at the IRIS DMC. Searchable metadata are extracted from the XML and enable powerful searches for products from EarthScope and other data sources. IRIS is teaming with the External Research Group at Microsoft Research to leverage a powerful Scientific Workflow Engine (Trident) and interact with the web services developed at centers such as IRIS to enable access to data services as well as computational services. We believe that this approach will allow web- based control of workflows and the invocation of computational services that transform data. This capability will greatly improve access to data across scientific disciplines. This presentation will review some of the traditional access tools as well as many of the newer approaches that use web services, scientific workflow to improve interdisciplinary data access.

TMATS/ IHAL/ DDML Schema Validation

DTIC Science & Technology

2017-02-01

task was to create a method for performing IRIG eXtensible Markup Language (XML) schema validation. As opposed to XML instance document validation...TMATS / IHAL / DDML Schema Validation, RCC 126-17, February 2017 vii Acronyms DDML Data Display Markup Language HUD heads-up display iNET...system XML eXtensible Markup Language TMATS / IHAL / DDML Schema Validation, RCC 126-17, February 2017 viii This page intentionally left blank

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

PubMed

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.

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Implementing a Rule-Based Contract Compliance Checker

NASA Astrophysics Data System (ADS)

Strano, Massimo; Molina-Jimenez, Carlos; Shrivastava, Santosh

The paper describes the design and implementation of an independent, third party contract monitoring service called Contract Compliance Checker (CCC). The CCC is provided with the specification of the contract in force, and is capable of observing and logging the relevant business-to-business (B2B) interaction events, in order to determine whether the actions of the business partners are consistent with the contract. A contract specification language called EROP (for Events, Rights, Obligations and Prohibitions) for the CCC has been developed based on business rules, that provides constructs to specify what rights, obligation and prohibitions become active and inactive after the occurrence of events related to the execution of business operations. The system has been designed to work with B2B industry standards such as ebXML and RosettaNet.

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

PubMed Central

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

Performance evaluation of continuity of care records (CCRs): parsing models in a mobile health management system.

PubMed

Chen, Hung-Ming; Liou, Yong-Zan

2014-10-01

In a mobile health management system, mobile devices act as the application hosting devices for personal health records (PHRs) and the healthcare servers construct to exchange and analyze PHRs. One of the most popular PHR standards is continuity of care record (CCR). The CCR is expressed in XML formats. However, parsing is an expensive operation that can degrade XML processing performance. Hence, the objective of this study was to identify different operational and performance characteristics for those CCR parsing models including the XML DOM parser, the SAX parser, the PULL parser, and the JSON parser with regard to JSON data converted from XML-based CCR. Thus, developers can make sensible choices for their target PHR applications to parse CCRs when using mobile devices or servers with different system resources. Furthermore, the simulation experiments of four case studies are conducted to compare the parsing performance on Android mobile devices and the server with large quantities of CCR data.

Facility Composer (Trademark) and PACES (Trademark) Integration: Development of an XML Interface Based on Industry Foundation Classes

DTIC Science & Technology

2007-11-01

Engineer- ing Research Laboratory is currently developing a set of facility ‘architec- tural’ programming tools , called Facility ComposerTM (FC). FC...requirements in the early phases of project development. As the facility program, crite- ria, and requirements are chosen, these tools populate the IFC...developing a set of facility “ar- chitectural” programming tools , called Facility Composer (FC), to support the capture and tracking of facility criteria

Integrating digital educational content created and stored within disparate software environments: an extensible markup language (XML) solution in real-world use.

PubMed

Frank, M S; Schultz, T; Dreyer, K

2001-06-01

To provide a standardized and scaleable mechanism for exchanging digital radiologic educational content between software systems that use disparate authoring, storage, and presentation technologies. Our institution uses two distinct software systems for creating educational content for radiology. Each system is used to create in-house educational content as well as commercial educational products. One system is an authoring and viewing application that facilitates the input and storage of hierarchical knowledge and associated imagery, and is capable of supporting a variety of entity relationships. This system is primarily used for the production and subsequent viewing of educational CD-ROMS. Another software system is primarily used for radiologic education on the world wide web. This system facilitates input and storage of interactive knowledge and associated imagery, delivering this content over the internet in a Socratic manner simulating in-person interaction with an expert. A subset of knowledge entities common to both systems was derived. An additional subset of knowledge entities that could be bidirectionally mapped via algorithmic transforms was also derived. An extensible markup language (XML) object model and associated lexicon were then created to represent these knowledge entities and their interactive behaviors. Forward-looking attention was exercised in the creation of the object model in order to facilitate straightforward future integration of other sources of educational content. XML generators and interpreters were written for both systems. Deriving the XML object model and lexicon was the most critical and time-consuming aspect of the project. The coding of the XML generators and interpreters required only a few hours for each environment. Subsequently, the transfer of hundreds of educational cases and thematic presentations between the systems can now be accomplished in a matter of minutes. The use of algorithmic transforms results in nearly 100% transfer of context as well as content, thus providing "presentation-ready" outcomes. The automation of knowledge exchange between dissimilar digital teaching environments magnifies the efforts of educators and enriches the learning experience for participants. XML is a powerful and useful mechanism for transfering educational content, as well as the context and interactive behaviors of such content, between disparate systems.

XML and Bibliographic Data: The TVS (Transport, Validation and Services) Model.

ERIC Educational Resources Information Center

de Carvalho, Joaquim; Cordeiro, Maria Ines

This paper discusses the role of XML in library information systems at three major levels: as are presentation language that enables the transport of bibliographic data in a way that is technologically independent and universally understood across systems and domains; as a language that enables the specification of complex validation rules…

XML Based Scientific Data Management Facility

NASA Technical Reports Server (NTRS)

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.

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

NASA Technical Reports Server (NTRS)

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.

JCMT observatory control system

NASA Astrophysics Data System (ADS)

Rees, Nicholas P.; Economou, Frossie; Jenness, Tim; Kackley, Russell D.; Walther, Craig A.; Dent, William R. F.; Folger, Martin; Gao, Xiaofeng; Kelly, Dennis; Lightfoot, John F.; Pain, Ian; Hovey, Gary J.; Redman, Russell O.

2002-12-01

The JCMT, the world's largest sub-mm telescope, has had essentially the same VAX/VMS based control system since it was commissioned. For the next generation of instrumentation we are implementing a new Unix/VxWorks based system, based on the successful ORAC system that was recently released on UKIRT. The system is now entering the integration and testing phase. This paper gives a broad overview of the system architecture and includes some discussion on the choices made. (Other papers in this conference cover some areas in more detail). The basic philosophy is to control the sub-systems with a small and simple set of commands, but passing detailed XML configuration descriptions along with the commands to give the flexibility required. The XML files can be passed between various layers in the system without interpretation, and so simplify the design enormously. This has all been made possible by the adoption of an Observation Preparation Tool, which essentially serves as an intelligent XML editor.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

PubMed Central

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

2012-01-01

Abstract 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. PMID:22357728

Astronomical Instrumentation System Markup Language

NASA Astrophysics Data System (ADS)

Goldbaum, Jesse M.

2016-05-01

The Astronomical Instrumentation System Markup Language (AISML) is an Extensible Markup Language (XML) based file format for maintaining and exchanging information about astronomical instrumentation. The factors behind the need for an AISML are first discussed followed by the reasons why XML was chosen as the format. Next it's shown how XML also provides the framework for a more precise definition of an astronomical instrument and how these instruments can be combined to form an Astronomical Instrumentation System (AIS). AISML files for several instruments as well as one for a sample AIS are provided. The files demonstrate how AISML can be utilized for various tasks from web page generation and programming interface to instrument maintenance and quality management. The advantages of widespread adoption of AISML are discussed.

Flight Dynamic Model Exchange using XML

NASA Technical Reports Server (NTRS)

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.

Spreadsheets for Analyzing and Optimizing Space Missions

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Agrawal, Anil K.; Czikmantory, Akos J.; Weisbin, Charles R.; Hua, Hook; Neff, Jon M.; Cowdin, Mark A.; Lewis, Brian S.; Iroz, Juana; Ross, Rick

2009-01-01

XCALIBR (XML Capability Analysis LIBRary) is a set of Extensible Markup Language (XML) database and spreadsheet- based analysis software tools designed to assist in technology-return-on-investment analysis and optimization of technology portfolios pertaining to outer-space missions. XCALIBR is also being examined for use in planning, tracking, and documentation of projects. An XCALIBR database contains information on mission requirements and technological capabilities, which are related by use of an XML taxonomy. XCALIBR incorporates a standardized interface for exporting data and analysis templates to an Excel spreadsheet. Unique features of XCALIBR include the following: It is inherently hierarchical by virtue of its XML basis. The XML taxonomy codifies a comprehensive data structure and data dictionary that includes performance metrics for spacecraft, sensors, and spacecraft systems other than sensors. The taxonomy contains >700 nodes representing all levels, from system through subsystem to individual parts. All entries are searchable and machine readable. There is an intuitive Web-based user interface. The software automatically matches technologies to mission requirements. The software automatically generates, and makes the required entries in, an Excel return-on-investment analysis software tool. The results of an analysis are presented in both tabular and graphical displays.

Distributed XQuery-Based Integration and Visualization of Multimodality Brain Mapping Data

PubMed Central

Detwiler, Landon T.; Suciu, Dan; Franklin, Joshua D.; Moore, Eider B.; Poliakov, Andrew V.; Lee, Eunjung S.; Corina, David P.; Ojemann, George A.; Brinkley, James F.

2008-01-01

This paper addresses the need for relatively small groups of collaborating investigators to integrate distributed and heterogeneous data about the brain. Although various national efforts facilitate large-scale data sharing, these approaches are generally too “heavyweight” for individual or small groups of investigators, with the result that most data sharing among collaborators continues to be ad hoc. Our approach to this problem is to create a “lightweight” distributed query architecture, in which data sources are accessible via web services that accept arbitrary query languages but return XML results. A Distributed XQuery Processor (DXQP) accepts distributed XQueries in which subqueries are shipped to the remote data sources to be executed, with the resulting XML integrated by DXQP. A web-based application called DXBrain accesses DXQP, allowing a user to create, save and execute distributed XQueries, and to view the results in various formats including a 3-D brain visualization. Example results are presented using distributed brain mapping data sources obtained in studies of language organization in the brain, but any other XML source could be included. The advantage of this approach is that it is very easy to add and query a new source, the tradeoff being that the user needs to understand XQuery and the schemata of the underlying sources. For small numbers of known sources this burden is not onerous for a knowledgeable user, leading to the conclusion that the system helps to fill the gap between ad hoc local methods and large scale but complex national data sharing efforts. PMID:19198662

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language

PubMed Central

Friedman, Carol; Hripcsak, George; Shagina, Lyuda; Liu, Hongfang

1999-01-01

Objective: To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. Methods: A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. Results: The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. Conclusions: Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available. PMID:9925230

A Flexible Online Metadata Editing and Management System

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

Aguilar, Raul; Pan, Jerry Yun; Gries, Corinna

2010-01-01

A metadata editing and management system is being developed employing state of the art XML technologies. A modular and distributed design was chosen for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool or schema walker used to generate code for the actual online editor, a native XML database, and an online user access management application. The design tool is a Java Swing application that reads an XML schema, provides the designer with options to combine input fields into online forms and give the fieldsmore » user friendly tags. Based on design decisions, the tool generates code for the online metadata editor. The code generated is an implementation of the XForms standard using the Orbeon Framework. The design tool fulfills two requirements: First, data entry forms based on one schema may be customized at design time and second data entry applications may be generated for any valid XML schema without relying on custom information in the schema. However, the customized information generated at design time is saved in a configuration file which may be re-used and changed again in the design tool. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services. Additional styling of the finished editor is accomplished via cascading style sheets which may be further customized and different look-and-feels may be accumulated through the community process. The customized editor produces XML files in compliance with the original schema, however, data from the current page is saved into a native XML database whenever the user moves to the next screen or pushes the save button independently of validity. Currently the system uses the open source XML database eXist for storage and management, which comes with third party online and desktop management tools. However, access to metadata files in the application introduced here is managed in a custom online module, using a MySQL backend accessed by a simple Java Server Faces front end. A flexible system with three grouping options, organization, group and single editing access is provided. Three levels were chosen to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.« less

RGG: A general GUI Framework for R scripts

PubMed Central

Visne, Ilhami; Dilaveroglu, Erkan; Vierlinger, Klemens; Lauss, Martin; Yildiz, Ahmet; Weinhaeusel, Andreas; Noehammer, Christa; Leisch, Friedrich; Kriegner, Albert

2009-01-01

Background R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required. Results We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) – tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR. Conclusion RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at PMID:19254356

An Efficient G-XML Data Management Method using XML Spatial Index for Mobile Devices

NASA Astrophysics Data System (ADS)

Tamada, Takashi; Momma, Kei; Seo, Kazuo; Hijikata, Yoshinori; Nishida, Shogo

This paper presents an efficient G-XML data management method for mobile devices. G-XML is XML based encoding for the transport of geographic information. Mobile devices, such as PDA and mobile-phone, performance trail desktop machines, so some techniques are needed for processing G-XML data on mobile devices. In this method, XML-format spatial index file is used to improve an initial display time of G-XML data. This index file contains XML pointer of each feature in G-XML data and classifies these features by multi-dimensional data structures. From the experimental result, we can prove this method speed up about 3-7 times an initial display time of G-XML data on mobile devices.

Speed up of XML parsers with PHP language implementation

NASA Astrophysics Data System (ADS)

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.

Internet-based data interchange with XML

NASA Astrophysics Data System (ADS)

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.

An XML-based system for the flexible classification and retrieval of clinical practice guidelines.

PubMed Central

Ganslandt, T.; Mueller, M. L.; Krieglstein, C. F.; Senninger, N.; Prokosch, H. U.

2002-01-01

Beneficial effects of clinical practice guidelines (CPGs) have not yet reached expectations due to limited routine adoption. Electronic distribution and reminder systems have the potential to overcome implementation barriers. Existing electronic CPG repositories like the National Guideline Clearinghouse (NGC) provide individual access but lack standardized computer-readable interfaces necessary for automated guideline retrieval. The aim of this paper was to facilitate automated context-based selection and presentation of CPGs. Using attributes from the NGC classification scheme, an XML-based metadata repository was successfully implemented, providing document storage, classification and retrieval functionality. Semi-automated extraction of attributes was implemented for the import of XML guideline documents using XPath. A hospital information system interface was exemplarily implemented for diagnosis-based guideline invocation. Limitations of the implemented system are discussed and possible future work is outlined. Integration of standardized computer-readable search interfaces into existing CPG repositories is proposed. PMID:12463831

XTCE and XML Database Evolution and Lessons from JWST, LandSat, and Constellation

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Kreistle, Steven; Fatig. Cirtos; Jones, Ronald

2008-01-01

The database organizations within three different NASA projects have advanced current practices by creating database synergy between the various spacecraft life cycle stakeholders and educating users in the benefits of the Consultative Committee for Space Data Systems (CCSDS) XML Telemetry and Command Exchange (XTCE) format. The combination of XML for managing program data and CCSDS XTCE for exchange is a robust approach that will meet all user requirements using Standards and Non proprietary tools. COTS tools for XTCEKML are very wide and varied. To combine together various low cost and free tools can be more expensive in the long run than choosing a more expensive COTS tool that meets all the needs. This was especially important when deploying in 32 remote sites with no need for licenses. A common mission XTCEKML format between dissimilar systems is possible and is not difficult. Command XMLKTCE is more complex than telemetry and the use of XTCEKML metadata to describe pages and scripts is needed due to the proprietary nature of most current ground systems. Other mission and science products such as spacecraft loads, science image catalogs, and mission operation procedures can all be described with XML as well to increase there flexibility as systems evolve and change. Figure 10 is an example of a spacecraft table load. The word is out and the XTCE community is growing, The f sXt TCE user group was held in October and in addition to ESAESOC, SC02000, and CNES identified several systems based on XTCE. The second XTCE user group is scheduled for March 10, 2008 with LDMC and others joining. As the experience with XTCE grows and the user community receives the promised benefits of using XTCE and XML the interest is growing fast.

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

Transparent ICD and DRG coding using information technology: linking and associating information sources with the eXtensible Markup Language.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or "semantically associated" parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach.

Transparent ICD and DRG Coding Using Information Technology: Linking and Associating Information Sources with the eXtensible Markup Language

PubMed Central

Hoelzer, Simon; Schweiger, Ralf K.; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or “semantically associated” parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach. PMID:12807813

Agility: Agent - Ility Architecture

DTIC Science & Technology

2002-10-01

existing and emerging standards (e.g., distributed objects, email, web, search engines , XML, Java, Jini). Three agent system components resulted from...agents and other Internet resources and operate over the web (AgentGram), a yellow pages service that uses Internet search engines to locate XML ads for agents and other Internet resources (WebTrader).

The semantic planetary data system

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Daniel; Kelly, Sean; Mattmann, Chris

2005-01-01

This paper will provide a brief overview of the PDS data model and the PDS catalog. It will then describe the implentation of the Semantic PDS including the development of the formal ontology, the generation of RDFS/XML and RDF/XML data sets, and the buiding of the semantic search application.

Using XML Configuration-Driven Development to Create a Customizable Ground Data System

NASA Technical Reports Server (NTRS)

Nash, Brent; DeMore, Martha

2009-01-01

The Mission data Processing and Control Subsystem (MPCS) is being developed as a multi-mission Ground Data System with the Mars Science Laboratory (MSL) as the first fully supported mission. MPCS is a fully featured, Java-based Ground Data System (GDS) for telecommand and telemetry processing based on Configuration-Driven Development (CDD). The eXtensible Markup Language (XML) is the ideal language for CDD because it is easily readable and editable by all levels of users and is also backed by a World Wide Web Consortium (W3C) standard and numerous powerful processing tools that make it uniquely flexible. The CDD approach adopted by MPCS minimizes changes to compiled code by using XML to create a series of configuration files that provide both coarse and fine grained control over all aspects of GDS operation.

IP telephony based danger alert communication system and its implementation

NASA Astrophysics Data System (ADS)

Rezac, Filip; Safarik, Jakub; Voznak, Miroslav; Tomala, Karel; Partila, Pavol

2013-05-01

This article discusses a danger alert system created as a part of the research project at Department of Telecommunications of Technical University of Ostrava. The aim of the system is to distribute pre-recorded voice messages in order to alert the called party in danger. This article describes individual technologies, which the application uses for its operation as well as issues relating to hardware requirements and transfer line bandwidth load. The article also describes new algorithms, which had to be developed in order to ensure the reliability of the system. Our intent is focused on disaster management, the message, which should be delivered within specified time span, is typed in the application and text-to-speech module ensures its transformation to a speech format, after that a particular scenario or warned area is selected and a target group is automatically unloaded. For this purpose, we have defined XML format for delivery of phone numbers which are located in the target area and these numbers are obtained from mobile BTS's (Base transmission stations). The benefit of such communication compared to others, is the fact, that it uses a phone call and, therefore, it is possible to get feedback who accepted the message and to improve efficiency of alert system. Finally, the list of unanswered calls is exported and these users can be informed via SMS.

XML under the Hood.

ERIC Educational Resources Information Center

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…

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

NASA Technical Reports Server (NTRS)

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. In our review of the database requirements and the COTS software available, only very expensive COTS software will meet 90% of requirements. Even with the high projected initial cost of COTS, the development and support for custom code over the 19-year mission period was forecasted to be higher than the total licensing costs. A group did look at reusing existing database tools and formats. If the JWST database was already in a mature state, the reuse made sense, but with the database still needing to handing the addition of different types of command and telemetry structures, defining new spacecraft systems, accept input and export to systems which has not been defined yet, XML provided the flexibility desired. It remains to be determined whether the XML database will reduce the over all cost for the JWST mission.

An adaptable XML based approach for scientific data management and integration

NASA Astrophysics Data System (ADS)

Wang, Fusheng; Thiel, Florian; Furrer, Daniel; Vergara-Niedermayr, Cristobal; Qin, Chen; Hackenberg, Georg; Bourgue, Pierre-Emmanuel; Kaltschmidt, David; Wang, Mo

2008-03-01

Increased complexity of scientific research poses new challenges to scientific data management. Meanwhile, scientific collaboration is becoming increasing important, which relies on integrating and sharing data from distributed institutions. We develop SciPort, a Web-based platform on supporting scientific data management and integration based on a central server based distributed architecture, where researchers can easily collect, publish, and share their complex scientific data across multi-institutions. SciPort provides an XML based general approach to model complex scientific data by representing them as XML documents. The documents capture not only hierarchical structured data, but also images and raw data through references. In addition, SciPort provides an XML based hierarchical organization of the overall data space to make it convenient for quick browsing. To provide generalization, schemas and hierarchies are customizable with XML-based definitions, thus it is possible to quickly adapt the system to different applications. While each institution can manage documents on a Local SciPort Server independently, selected documents can be published to a Central Server to form a global view of shared data across all sites. By storing documents in a native XML database, SciPort provides high schema extensibility and supports comprehensive queries through XQuery. By providing a unified and effective means for data modeling, data access and customization with XML, SciPort provides a flexible and powerful platform for sharing scientific data for scientific research communities, and has been successfully used in both biomedical research and clinical trials.

An Adaptable XML Based Approach for Scientific Data Management and Integration.

PubMed

Wang, Fusheng; Thiel, Florian; Furrer, Daniel; Vergara-Niedermayr, Cristobal; Qin, Chen; Hackenberg, Georg; Bourgue, Pierre-Emmanuel; Kaltschmidt, David; Wang, Mo

2008-02-20

Increased complexity of scientific research poses new challenges to scientific data management. Meanwhile, scientific collaboration is becoming increasing important, which relies on integrating and sharing data from distributed institutions. We develop SciPort, a Web-based platform on supporting scientific data management and integration based on a central server based distributed architecture, where researchers can easily collect, publish, and share their complex scientific data across multi-institutions. SciPort provides an XML based general approach to model complex scientific data by representing them as XML documents. The documents capture not only hierarchical structured data, but also images and raw data through references. In addition, SciPort provides an XML based hierarchical organization of the overall data space to make it convenient for quick browsing. To provide generalization, schemas and hierarchies are customizable with XML-based definitions, thus it is possible to quickly adapt the system to different applications. While each institution can manage documents on a Local SciPort Server independently, selected documents can be published to a Central Server to form a global view of shared data across all sites. By storing documents in a native XML database, SciPort provides high schema extensibility and supports comprehensive queries through XQuery. By providing a unified and effective means for data modeling, data access and customization with XML, SciPort provides a flexible and powerful platform for sharing scientific data for scientific research communities, and has been successfully used in both biomedical research and clinical trials.

Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

This paper discusses the detailed design of an XML databinding framework for aircraft engine simulation. The framework provides an object interface to access and use engine data. while at the same time preserving the meaning of the original data. The Language independent representation of engine component data enables users to move around XML data using HTTP through disparate networks. The application of this framework is demonstrated via a web-based turbofan propulsion system simulation using the World Wide Web (WWW). A Java Servlet based web component architecture is used for rendering XML engine data into HTML format and dealing with input events from the user, which allows users to interact with simulation data from a web browser. The simulation data can also be saved to a local disk for archiving or to restart the simulation at a later time.

An Electronic Finding Aid Using Extensible Markup Language (XML) and Encoded Archival Description (EAD).

ERIC Educational Resources Information Center

Chang, May

2000-01-01

Describes the development of electronic finding aids for archives at the University of Illinois, Urbana-Champaign that used XML (extensible markup language) and EAD (encoded archival description) to enable more flexible information management and retrieval than using MARC or a relational database management system. EAD template is appended.…

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

PubMed Central

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

Internet Patient Records: new techniques

PubMed Central

Moehrs, Sascha; Anedda, Paolo; Tuveri, Massimiliano; Zanetti, Gianluigi

2001-01-01

Background The ease by which the Internet is able to distribute information to geographically-distant users on a wide variety of computers makes it an obvious candidate for a technological solution for electronic patient record systems. Indeed, second-generation Internet technologies such as the ones described in this article - XML (eXtensible Markup Language), XSL (eXtensible Style Language), DOM (Document Object Model), CSS (Cascading Style Sheet), JavaScript, and JavaBeans - may significantly reduce the complexity of the development of distributed healthcare systems. Objective The demonstration of an experimental Electronic Patient Record (EPR) system built from those technologies that can support viewing of medical imaging exams and graphically-rich clinical reporting tools, while conforming to the newly emerging XML standard for digital documents. In particular, we aim to promote rapid prototyping of new reports by clinical specialists. Methods We have built a prototype EPR client, InfoDOM, that runs in both the popular web browsers. In this second version it receives each EPR as an XML record served via the secure SSL (Secure Socket Layer) protocol. JavaBean software components manipulate the XML to store it and then to transform it into a variety of useful clinical views. First a web page summary for the patient is produced. From that web page other JavaBeans can be launched. In particular, we have developed a medical imaging exam Viewer and a clinical Reporter bean parameterized appropriately for the particular patient and exam in question. Both present particular views of the XML data. The Viewer reads image sequences from a patient-specified network URL on a PACS (Picture Archiving and Communications System) server and presents them in a user-controllable animated sequence, while the Reporter provides a configurable anatomical map of the site of the pathology, from which individual "reportlets" can be launched. The specification of these reportlets is achieved using standard HTML forms and thus may conceivably be authored by clinical specialists. A generic JavaScript library has been written that allows the seamless incorporation of such contributions into the InfoDOM client. In conjunction with another JavaBean, that library renders graphically-enhanced reporting tools that read and write content to and from the XML data-structure, ready for resubmission to the EPR server. Results We demonstrate the InfoDOM experimental EPR system that is currently being adapted for test-bed use in three hospitals in Cagliari, Italy. For this we are working with specialists in neurology, radiology, and epilepsy. Conclusions Early indications are that the rapid prototyping of reports afforded by our EPR system can assist communication between clinical specialists and our system developers. We are now experimenting with new technologies that may provide services to the kind of XML EPR client described here. PMID:11720950

Structured Course Objects in a Digital Library

NASA Technical Reports Server (NTRS)

Maly, K.; Zubair, M.; Liu, X.; Nelson, M.; Zeil, S.

1999-01-01

We are developing an Undergraduate Digital Library Framework (UDLF) that will support creation/archiving of courses and reuse of existing course material to evolve courses. UDLF supports the publication of course materials for later instantiation for a specific offering and allows the addition of time-dependent and student-specific information and structures. Instructors and, depending on permissions, students can access the general course materials or the materials for a specific offering. We are building a reference implementation based on NCSTRL+, a digital library derived from NCSTRL. Digital objects in NCSTRL+ are called buckets, self-contained entities that carry their own methods for access and display. Current bucket implementations have a two level structure of packages and elements. This is not a rich enough structure for course objects in UDLF. Typically, courses can only be modeled as a multilevel hierarchy and among different courses, both the syntax and semantics of terms may vary. Therefore, we need a mechanism to define, within a particular library, course models, their constituent objects, and the associated semantics in a flexible, extensible way. In this paper, we describe our approach to define and implement these multilayered course objects. We use XML technology to emulate complex data structures within the NCSTRL+ buckets. We have developed authoring and browsing tools to manipulate these course objects. In our current implementation a user downloading an XML based course bucket also downloads the XML-aware tools: an applet that enables the user to edit or browse the bucket. We claim that XML provides an effective means to represent multi-level structure of a course bucket.

Enhanced Product Generation at NASA Data Centers Through Grid Technology

NASA Technical Reports Server (NTRS)

Barkstrom, Bruce R.; Hinke, Thomas H.; Gavali, Shradha; Seufzer, William J.

2003-01-01

This paper describes how grid technology can support the ability of NASA data centers to provide customized data products. A combination of grid technology and commodity processors are proposed to provide the bandwidth necessary to perform customized processing of data, with customized data subsetting providing the initial example. This customized subsetting engine can be used to support a new type of subsetting, called phenomena-based subsetting, where data is subsetted based on its association with some phenomena, such as mesoscale convective systems or hurricanes. This concept is expanded to allow the phenomena to be detected in one type of data, with the subsetting requirements transmitted to the subsetting engine to subset a different type of data. The subsetting requirements are generated by a data mining system and transmitted to the subsetter in the form of an XML feature index that describes the spatial and temporal extent of the phenomena. For this work, a grid-based mining system called the Grid Miner is used to identify the phenomena and generate the feature index. This paper discusses the value of grid technology in facilitating the development of a high performance customized product processing and the coupling of a grid mining system to support phenomena-based subsetting.

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

PubMed

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.

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

PubMed

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

PubMed Central

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

2015-01-01

Motivation 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. Results 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. Availability 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. PMID:25927999

Using XML to encode TMA DES metadata.

PubMed

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

PubMed Central

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

KAT: A Flexible XML-based Knowledge Authoring Environment

PubMed Central

Hulse, Nathan C.; Rocha, Roberto A.; Del Fiol, Guilherme; Bradshaw, Richard L.; Hanna, Timothy P.; Roemer, Lorrie K.

2005-01-01

As part of an enterprise effort to develop new clinical information systems at Intermountain Health Care, the authors have built a knowledge authoring tool that facilitates the development and refinement of medical knowledge content. At present, users of the application can compose order sets and an assortment of other structured clinical knowledge documents based on XML schemas. The flexible nature of the application allows the immediate authoring of new types of documents once an appropriate XML schema and accompanying Web form have been developed and stored in a shared repository. The need for a knowledge acquisition tool stems largely from the desire for medical practitioners to be able to write their own content for use within clinical applications. We hypothesize that medical knowledge content for clinical use can be successfully created and maintained through XML-based document frameworks containing structured and coded knowledge. PMID:15802477

A Semantic Analysis of XML Schema Matching for B2B Systems Integration

ERIC Educational Resources Information Center

Kim, Jaewook

2011-01-01

One of the most critical steps to integrating heterogeneous e-Business applications using different XML schemas is schema matching, which is known to be costly and error-prone. Many automatic schema matching approaches have been proposed, but the challenge is still daunting because of the complexity of schemas and immaturity of technologies in…

Convergence of Health Level Seven Version 2 Messages to Semantic Web Technologies for Software-Intensive Systems in Telemedicine Trauma Care.

PubMed

Menezes, Pedro Monteiro; Cook, Timothy Wayne; Cavalini, Luciana Tricai

2016-01-01

To present the technical background and the development of a procedure that enriches the semantics of Health Level Seven version 2 (HL7v2) messages for software-intensive systems in telemedicine trauma care. This study followed a multilevel model-driven approach for the development of semantically interoperable health information systems. The Pre-Hospital Trauma Life Support (PHTLS) ABCDE protocol was adopted as the use case. A prototype application embedded the semantics into an HL7v2 message as an eXtensible Markup Language (XML) file, which was validated against an XML schema that defines constraints on a common reference model. This message was exchanged with a second prototype application, developed on the Mirth middleware, which was also used to parse and validate both the original and the hybrid messages. Both versions of the data instance (one pure XML, one embedded in the HL7v2 message) were equally validated and the RDF-based semantics recovered by the receiving side of the prototype from the shared XML schema. This study demonstrated the semantic enrichment of HL7v2 messages for intensive-software telemedicine systems for trauma care, by validating components of extracts generated in various computing environments. The adoption of the method proposed in this study ensures the compliance of the HL7v2 standard in Semantic Web technologies.

Symmetric Key Services Markup Language (SKSML)

NASA Astrophysics Data System (ADS)

Noor, Arshad

Symmetric Key Services Markup Language (SKSML) is the eXtensible Markup Language (XML) being standardized by the OASIS Enterprise Key Management Infrastructure Technical Committee for requesting and receiving symmetric encryption cryptographic keys within a Symmetric Key Management System (SKMS). This protocol is designed to be used between clients and servers within an Enterprise Key Management Infrastructure (EKMI) to secure data, independent of the application and platform. Building on many security standards such as XML Signature, XML Encryption, Web Services Security and PKI, SKSML provides standards-based capability to allow any application to use symmetric encryption keys, while maintaining centralized control. This article describes the SKSML protocol and its capabilities.

Knowledge representation for fuzzy inference aided medical image interpretation.

PubMed

Gal, Norbert; Stoicu-Tivadar, Vasile

2012-01-01

Knowledge defines how an automated system transforms data into information. This paper suggests a representation method of medical imaging knowledge using fuzzy inference systems coded in XML files. The imaging knowledge incorporates features of the investigated objects in linguistic form and inference rules that can transform the linguistic data into information about a possible diagnosis. A fuzzy inference system is used to model the vagueness of the linguistic medical imaging terms. XML files are used to facilitate easy manipulation and deployment of the knowledge into the imaging software. Preliminary results are presented.

Distribution of immunodeficiency fact files with XML--from Web to WAP.

PubMed

Väliaho, Jouni; Riikonen, Pentti; Vihinen, Mauno

2005-06-26

Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at http://bioinf.uta.fi/idr/. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at http://bioinf.uta.fi/idml/.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Global Location-Based Access to Web Applications Using Atom-Based Automatic Update

NASA Astrophysics Data System (ADS)

Singh, Kulwinder; Park, Dong-Won

We propose an architecture which enables people to enquire about information available in directory services by voice using regular phones. We implement a Virtual User Agent (VUA) which mediates between the human user and a business directory service. The system enables the user to search for the nearest clinic, gas station by price, motel by price, food / coffee, banks/ATM etc. and fix an appointment, or automatically establish a call between the user and the business party if the user prefers. The user also has an option to receive appointment confirmation by phone, SMS, or e-mail. The VUA is accessible by a toll free DID (Direct Inward Dialing) number using a phone by anyone, anywhere, anytime. We use the Euclidean formula for distance measurement. Since, shorter geodesic distances (on the Earth’s surface) correspond to shorter Euclidean distances (measured by a straight line through the Earth). Our proposed architecture uses Atom XML syndication format protocol for data integration, VoiceXML for creating the voice user interface (VUI) and CCXML for controlling the call components. We also provide an efficient algorithm for parsing Atom feeds which provide data to the system. Moreover, we describe a cost-effective way for providing global access to the VUA based on Asterisk (an open source IP-PBX). We also provide some information on how our system can be integrated with GPS for locating the user coordinates and therefore efficiently and spontaneously enhancing the system response. Additionally, the system has a mechanism for validating the phone numbers in its database, and it updates the number and other information such as daily price of gas, motel etc. automatically using an Atom-based feed. Currently, the commercial directory services (Example 411) do not have facilities to update the listing in the database automatically, so that why callers most of the times get out-of-date phone numbers or other information. Our system can be integrated very easily with an existing web infrastructure, thereby making the wealth of Web information easily available to the user by phone. This kind of system can be deployed as an extension to 911 and 411 services to share the workload with human operators. This paper presents all the underlying principles, architecture, features, and an example of the real world deployment of our proposed system. The source code and documentations are available for commercial productions.

A Space Surveillance Ontology: Captured in an XML Schema

DTIC Science & Technology

2000-10-01

characterization in a way most appropriate to a sub- domain. 6. The commercial market is embracing XML, and the military can take advantage of this significant...the space surveillance ontology effort to two key efforts: the Defense Information Infrastructure Common Operating Environment (DII COE) XML...strongly believe XML schemas will supplant them. Some of the advantages that XML schemas provide over DTDs include: • Strong data typing: The XML Schema

A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML).

PubMed

Kottmann, Renzo; Gray, Tanya; Murphy, Sean; Kagan, Leonid; Kravitz, Saul; Lombardot, Thierry; Field, Dawn; Glöckner, Frank Oliver

2008-06-01

The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the "Minimum Information about a Genome Sequence" (MIGS) specification and its extension, the "Minimum Information about a Metagenome Sequence" (MIMS). GCDML is an XML Schema for generating MIGS/MIMS compliant reports for data entry, exchange, and storage. When mature, this sample-centric, strongly-typed schema will provide a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. Here we describe the need for such a project, outline design principles required to support the project, and make an open call for participation in defining the future content of GCDML. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).

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

PubMed

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.

Activate/Inhibit KGCS Gateway via Master Console EIC Pad-B Display

NASA Technical Reports Server (NTRS)

Ferreira, Pedro Henrique

2014-01-01

My internship consisted of two major projects for the Launch Control System.The purpose of the first project was to implement the Application Control Language (ACL) to Activate Data Acquisition (ADA) and to Inhibit Data Acquisition (IDA) the Kennedy Ground Control Sub-Systems (KGCS) Gateway, to update existing Pad-B End Item Control (EIC) Display to program the ADA and IDA buttons with new ACL, and to test and release the ACL Display.The second project consisted of unit testing all of the Application Services Framework (ASF) by March 21st. The XmlFileReader was unit tested and reached 100 coverage. The XmlFileReader class is used to grab information from XML files and use them to initialize elements in the other framework elements by using the Xerces C++ XML Parser; which is open source commercial off the shelf software. The ScriptThread was also tested. ScriptThread manages the creation and activation of script threads. A large amount of the time was used in initializing the environment and learning how to set up unit tests and getting familiar with the specific segments of the project that were assigned to us.

Production Experiences with the Cray-Enabled TORQUE Resource Manager

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

Ezell, Matthew A; Maxwell, Don E; Beer, David

High performance computing resources utilize batch systems to manage the user workload. Cray systems are uniquely different from typical clusters due to Cray s Application Level Placement Scheduler (ALPS). ALPS manages binary transfer, job launch and monitoring, and error handling. Batch systems require special support to integrate with ALPS using an XML protocol called BASIL. Previous versions of Adaptive Computing s TORQUE and Moab batch suite integrated with ALPS from within Moab, using PERL scripts to interface with BASIL. This would occasionally lead to problems when all the components would become unsynchronized. Version 4.1 of the TORQUE Resource Manager introducedmore » new features that allow it to directly integrate with ALPS using BASIL. This paper describes production experiences at Oak Ridge National Laboratory using the new TORQUE software versions, as well as ongoing and future work to improve TORQUE.« less

An enhanced security solution for electronic medical records based on AES hybrid technique with SOAP/XML and SHA-1.

PubMed

Kiah, M L Mat; Nabi, Mohamed S; Zaidan, B B; Zaidan, A A

2013-10-01

This study aims to provide security solutions for implementing electronic medical records (EMRs). E-Health organizations could utilize the proposed method and implement recommended solutions in medical/health systems. Majority of the required security features of EMRs were noted. The methods used were tested against each of these security features. In implementing the system, the combination that satisfied all of the security features of EMRs was selected. Secure implementation and management of EMRs facilitate the safeguarding of the confidentiality, integrity, and availability of e-health organization systems. Health practitioners, patients, and visitors can use the information system facilities safely and with confidence anytime and anywhere. After critically reviewing security and data transmission methods, a new hybrid method was proposed to be implemented on EMR systems. This method will enhance the robustness, security, and integration of EMR systems. The hybrid of simple object access protocol/extensible markup language (XML) with advanced encryption standard and secure hash algorithm version 1 has achieved the security requirements of an EMR system with the capability of integrating with other systems through the design of XML messages.

ScotlandsPlaces XML: Bespoke XML or XML Mapping?

ERIC Educational Resources Information Center

Beamer, Ashley; Gillick, Mark

2010-01-01

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

An Introduction to the Extensible Markup Language (XML).

ERIC Educational Resources Information Center

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)

XML Reconstruction View Selection in XML Databases: Complexity Analysis and Approximation Scheme

NASA Astrophysics Data System (ADS)

Chebotko, Artem; Fu, Bin

Query evaluation in an XML database requires reconstructing XML subtrees rooted at nodes found by an XML query. Since XML subtree reconstruction can be expensive, one approach to improve query response time is to use reconstruction views - materialized XML subtrees of an XML document, whose nodes are frequently accessed by XML queries. For this approach to be efficient, the principal requirement is a framework for view selection. In this work, we are the first to formalize and study the problem of XML reconstruction view selection. The input is a tree T, in which every node i has a size c i and profit p i , and the size limitation C. The target is to find a subset of subtrees rooted at nodes i 1, ⋯ , i k respectively such that c_{i_1}+\\cdots +c_{i_k}le C, and p_{i_1}+\\cdots +p_{i_k} is maximal. Furthermore, there is no overlap between any two subtrees selected in the solution. We prove that this problem is NP-hard and present a fully polynomial-time approximation scheme (FPTAS) as a solution.

An Extended Petri-Net Based Approach for Supply Chain Process Enactment in Resource-Centric Web Service Environment

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Zhang, Xiaoyu; Cai, Hongming; Xu, Boyi

Enacting a supply-chain process involves variant partners and different IT systems. REST receives increasing attention for distributed systems with loosely coupled resources. Nevertheless, resource model incompatibilities and conflicts prevent effective process modeling and deployment in resource-centric Web service environment. In this paper, a Petri-net based framework for supply-chain process integration is proposed. A resource meta-model is constructed to represent the basic information of resources. Then based on resource meta-model, XML schemas and documents are derived, which represent resources and their states in Petri-net. Thereafter, XML-net, a high level Petri-net, is employed for modeling control and data flow of process. From process model in XML-net, RESTful services and choreography descriptions are deduced. Therefore, unified resource representation and RESTful services description are proposed for cross-system integration in a more effective way. A case study is given to illustrate the approach and the desirable features of the approach are discussed.

XML Based Scientific Data Management Facility

NASA Technical Reports Server (NTRS)

Mehrotra, Piyush; Zubair, M.; Ziebartt, John (Technical Monitor)

2001-01-01

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 HTML 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.

Non-invasive lightweight integration engine for building EHR from autonomous distributed systems.

PubMed

Angulo, Carlos; Crespo, Pere; Maldonado, José A; Moner, David; Pérez, Daniel; Abad, Irene; Mandingorra, Jesús; Robles, Montserrat

2007-12-01

In this paper we describe Pangea-LE, a message-oriented lightweight data integration engine that allows homogeneous and concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and passes it to the requesting client applications in a flexible XML format. The XML response message can be formatted on demand by appropriate Extensible Stylesheet Language (XSL) transformations in order to meet the needs of client applications. We also present a real deployment in a hospital where Pangea-LE collects and generates an XML view of all the available patient clinical information. The information is presented to healthcare professionals in an Electronic Health Record (EHR) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real setting has been a success due to the non-invasive nature of Pangea-LE which respects the existing information systems.

Convergence of Health Level Seven Version 2 Messages to Semantic Web Technologies for Software-Intensive Systems in Telemedicine Trauma Care

PubMed Central

Cook, Timothy Wayne; Cavalini, Luciana Tricai

2016-01-01

Objectives To present the technical background and the development of a procedure that enriches the semantics of Health Level Seven version 2 (HL7v2) messages for software-intensive systems in telemedicine trauma care. Methods This study followed a multilevel model-driven approach for the development of semantically interoperable health information systems. The Pre-Hospital Trauma Life Support (PHTLS) ABCDE protocol was adopted as the use case. A prototype application embedded the semantics into an HL7v2 message as an eXtensible Markup Language (XML) file, which was validated against an XML schema that defines constraints on a common reference model. This message was exchanged with a second prototype application, developed on the Mirth middleware, which was also used to parse and validate both the original and the hybrid messages. Results Both versions of the data instance (one pure XML, one embedded in the HL7v2 message) were equally validated and the RDF-based semantics recovered by the receiving side of the prototype from the shared XML schema. Conclusions This study demonstrated the semantic enrichment of HL7v2 messages for intensive-software telemedicine systems for trauma care, by validating components of extracts generated in various computing environments. The adoption of the method proposed in this study ensures the compliance of the HL7v2 standard in Semantic Web technologies. PMID:26893947

Automated Test Methods for XML Metadata

DTIC Science & Technology

2017-12-28

Group under RCC Task TG-147. This document (Volume VI of the RCC Document 118 series) describes procedures used for evaluating XML metadata documents...including TMATS, MDL, IHAL, and DDML documents. These documents contain specifications or descriptions of artifacts and systems of importance to...the collection and management of telemetry data. The methods defined in this report provide a means of evaluating the suitability of such a metadata

Schema for Spacecraft-Command Dictionary

NASA Technical Reports Server (NTRS)

Laubach, Sharon; Garcia, Celina; Maxwell, Scott; Wright, Jesse

2008-01-01

An Extensible Markup Language (XML) schema was developed as a means of defining and describing a structure for capturing spacecraft command- definition and tracking information in a single location in a form readable by both engineers and software used to generate software for flight and ground systems. A structure defined within this schema is then used as the basis for creating an XML file that contains command definitions.

At-sea demonstration of RF sensor tasking using XML over a worldwide network

NASA Astrophysics Data System (ADS)

Kellogg, Robert L.; Lee, Tom; Dumas, Diane; Raggo, Barbara

2003-07-01

As part of an At-Sea Demonstration for Space and Naval Warfare Command (SPAWAR, PMW-189), a prototype RF sensor for signal acquisition and direction finding queried and received tasking via a secure worldwide Automated Data Network System (ADNS). Using extended mark-up language (XML) constructs, both mission and signal tasking were available for push and pull Battlespace management. XML tasking was received by the USS Cape St George (CG-71) during an exercise along the Gulf Coast of the US from a test facility at SPAWAR, San Diego, CA. Although only one ship was used in the demonstration, the intent of the software initiative was to show that a network of different RF sensors on different platforms with different capabilitis could be tasked by a common web agent. A sensor software agent interpreted the XML task to match the sensor's capability. Future improvements will focus on enlarging the domain of mission tasking and incorporate report management.

XML, Ontologies, and Their Clinical Applications.

PubMed

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.

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

PubMed

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.

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

ERIC Educational Resources Information Center

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…

SU-E-T-406: Use of TrueBeam Developer Mode and API to Increase the Efficiency and Accuracy of Commissioning Measurements for the Varian EDGE Stereotactic Linac

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

Gardner, S; Gulam, M; Song, K

2014-06-01

Purpose: The Varian EDGE machine is a new stereotactic platform, combining Calypso and VisionRT localization systems with a stereotactic linac. The system includes TrueBeam DeveloperMode, making possible the use of XML-scripting for automation of linac-related tasks. This study details the use of DeveloperMode to automate commissioning tasks for Varian EDGE, thereby improving efficiency and measurement consistency. Methods: XML-scripting was used for various commissioning tasks,including couch model verification,beam-scanning,and isocenter verification. For couch measurements, point measurements were acquired for several field sizes (2×2,4×4,10×10cm{sup 2}) at 42 gantry angles for two couch-models. Measurements were acquired with variations in couch position(rails in/out,couch shifted inmore » each of motion axes) compared to treatment planning system(TPS)-calculated values,which were logged automatically through advanced planning interface(API) scripting functionality. For beam scanning, XML-scripts were used to create custom MLC-apertures. For isocenter verification, XML-scripts were used to automate various Winston-Lutz-type tests. Results: For couch measurements, the time required for each set of angles was approximately 9 minutes. Without scripting, each set required approximately 12 minutes. Automated measurements required only one physicist, while manual measurements required at least two physicists to handle linac positions/beams and data recording. MLC apertures were generated outside of the TPS,and with the .xml file format, double-checking without use of TPS/operator console was possible. Similar time efficiency gains were found for isocenter verification measurements Conclusion: The use of XML scripting in TrueBeam DeveloperMode allows for efficient and accurate data acquisition during commissioning. The efficiency improvement is most pronounced for iterative measurements, exemplified by the time savings for couch modeling measurements(approximately 10 hours). The scripting also allowed for creation of the files in advance without requiring access to TPS. The API scripting functionality enabled efficient creation/mining of TPS data. Finally, automation reduces the potential for human error in entering linac values at the machine console,and the script provides a log of measurements acquired for each session. This research was supported in part by a grant from Varian Medical Systems, Palo Alto, CA.« less

Developing and integrating an adverse drug reaction reporting system with the hospital information system.

PubMed

Kataoka, Satoshi; Ohe, Kazuhiko; Mochizuki, Mayumi; Ueda, Shiro

2002-01-01

We have developed an adverse drug reaction (ADR) reporting system integrating it with Hospital Information System (HIS) of the University of Tokyo Hospital. Since this system is designed with JAVA, it is portable without re-compiling to any operating systems on which JAVA virtual machines work. In this system, we implemented an automatic data filling function using XML-based (extended Markup Language) files generated by HIS. This new specification would decrease the time needed for physicians and pharmacists to fill the spontaneous ADR reports. By clicking a button, the report is sent to the text database through Simple Mail Transfer Protocol (SMTP) electronic mails. The destination of the report mail can be changed arbitrarily by administrators, which adds this system more flexibility for practical operation. Although we tried our best to use the SGML-based (Standard Generalized Markup Language) ICH M2 guideline to follow the global standard of the case report, we eventually adopted XML as the output report format. This is because we found some problems in handling two bytes characters with ICH guideline and XML has a lot of useful features. According to our pilot survey conducted at the University of Tokyo Hospital, many physicians answered that our idea, integrating ADR reporting system to HIS, would increase the ADR reporting numbers.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

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

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

Pathology data integration with eXtensible Markup Language.

PubMed

Berman, Jules J

2005-02-01

It is impossible to overstate the importance of XML (eXtensible Markup Language) as a data organization tool. With XML, pathologists can annotate all of their data (clinical and anatomic) in a format that can transform every pathology report into a database, without compromising narrative structure. The purpose of this manuscript is to provide an overview of XML for pathologists. Examples will demonstrate how pathologists can use XML to annotate individual data elements and to structure reports in a common format that can be merged with other XML files or queried using standard XML tools. This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases.

OPSO - The OpenGL based Field Acquisition and Telescope Guiding System

NASA Astrophysics Data System (ADS)

Škoda, P.; Fuchs, J.; Honsa, J.

2006-07-01

We present OPSO, a modular pointing and auto-guiding system for the coudé spectrograph of the Ondřejov observatory 2m telescope. The current field and slit viewing CCD cameras with image intensifiers are giving only standard TV video output. To allow the acquisition and guiding of very faint targets, we have designed an image enhancing system working in real time on TV frames grabbed by BT878-based video capture card. Its basic capabilities include the sliding averaging of hundreds of frames with bad pixel masking and removal of outliers, display of median of set of frames, quick zooming, contrast and brightness adjustment, plotting of horizontal and vertical cross cuts of seeing disk within given intensity range and many more. From the programmer's point of view, the system consists of three tasks running in parallel on a Linux PC. One C task controls the video capturing over Video for Linux (v4l2) interface and feeds the frames into the large block of shared memory, where the core image processing is done by another C program calling the OpenGL library. The GUI is, however, dynamically built in Python from XML description of widgets prepared in Glade. All tasks are exchanging information by IPC calls using the shared memory segments.

A Framework for Resilient Remote Monitoring

DTIC Science & Technology

2014-08-01

of low-level observables are availa- ble, audited , and recorded. This establishes the need for a re- mote monitoring framework that can integrate with...Security, WS-Policy, SAML, XML Signature, and XML Encryption. Pearson Higher Education, 2004. [3] OMG, “Common Secure Interoperability Protocol...www.darpa.mil/Our_Work/I2O/Programs/Integrated_Cyb er_Analysis_System_%28ICAS%29.aspx. [8] D. Miller and B. Pearson , Security information and event man

Toward XML Representation of NSS Simulation Scenario for Mission Scenario Exchange Capability

DTIC Science & Technology

2003-09-01

app.html Deitel , H. M., Deitel , P. J., Nieto, T. R., Lin, T. M., Sadhu, P. (2001). XML How to Program . Upper Saddle River: Prentice Hall...Combat XXI Program ...........................13 2. Transition NSS to a Java Environment ...........................................13 3. Shift to an...STATEMENT The Naval Simulation System (NSS) is a powerful computer program developed by the Navy to provide a force-on-force modeling and simulation

phyloXML: XML for evolutionary biology and comparative genomics

PubMed Central

Han, Mira V; Zmasek, Christian M

2009-01-01

Background 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. Results 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. Conclusion 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 . PMID:19860910

A Solution to Metadata: Using XML Transformations to Automate Metadata

DTIC Science & Technology

2010-06-01

developed their own metadata standards—Directory Interchange Format (DIF), Ecological Metadata Language ( EML ), and International Organization for...mented all their data using the EML standard. However, when later attempting to publish to a data clearinghouse— such as the Geospatial One-Stop (GOS...construct calls to its transform(s) method by providing the type of the incoming content (e.g., eml ), the type of the resulting content (e.g., fgdc) and

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

NASA Astrophysics Data System (ADS)

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 Files

MedlinePlus

... this page, please enable JavaScript. MedlinePlus produces XML data sets that you are welcome to download and use. If you have questions about the MedlinePlus XML files, please contact us . For additional sources of MedlinePlus data in XML format, visit our Web service page, ...

TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

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

Mishra, P; Varian Medical Systems, Palo Alto, CA; Lewis, J

2014-06-15

Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slotsmore » mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future developments and collaboration with other researchers. I am an employee of Varian Medical Systems.« less

XML and E-Journals: The State of Play.

ERIC Educational Resources Information Center

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…

Integrated Array/Metadata Analytics

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Baumann, Peter

2015-04-01

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

WITH: a system to write clinical trials using XML and RDBMS.

PubMed Central

Fazi, Paola; Luzi, Daniela; Manco, Mariarosaria; Ricci, Fabrizio L.; Toffoli, Giovanni; Vignetti, Marco

2002-01-01

The paper illustrates the system WITH (Write on Internet clinical Trials in Haematology) which supports the writing of a clinical trial (CT) document. The requirements of this system have been defined analysing the writing process of a CT and then modelling the content of its sections together with their logical and temporal relationships. The system WITH allows: a) editing the document text; b) re-using the text; and c) facilitating the cooperation and the collaborative writing. It is based on XML mark-up language, and on a RDBMS. This choice guarantees: a) process standardisation; b) process management; c) efficient delivery of information-based tasks; and d) explicit focus on process design. PMID:12463823

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

PubMed

Döring, Kersten; Grüning, Björn A; Telukunta, Kiran K; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user's system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects.

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

PubMed Central

Döring, Kersten; Grüning, Björn A.; Telukunta, Kiran K.; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user’s system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects. PMID:27706202

User-Friendly Interface Developed for a Web-Based Service for SpaceCAL Emulations

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

A team at the NASA Glenn Research Center is developing a Space Communications Architecture Laboratory (SpaceCAL) for protocol development activities for coordinated satellite missions. SpaceCAL will provide a multiuser, distributed system to emulate space-based Internet architectures, backbone networks, formation clusters, and constellations. As part of a new effort in 2003, building blocks are being defined for an open distributed system to make the satellite emulation test bed accessible through an Internet connection. The first step in creating a Web-based service to control the emulation remotely is providing a user-friendly interface for encoding the data into a well-formed and complete Extensible Markup Language (XML) document. XML provides coding that allows data to be transferred between dissimilar systems. Scenario specifications include control parameters, network routes, interface bandwidths, delay, and bit error rate. Specifications for all satellite, instruments, and ground stations in a given scenario are also included in the XML document. For the SpaceCAL emulation, the XML document can be created using XForms, a Webbased forms language for data collection. Contrary to older forms technology, the interactive user interface makes the science prevalent, not the data representation. Required versus optional input fields, default values, automatic calculations, data validation, and reuse will help researchers quickly and accurately define missions. XForms can apply any XML schema defined for the test mission to validate data before forwarding it to the emulation facility. New instrument definitions, facilities, and mission types can be added to the existing schema. The first prototype user interface incorporates components for interactive input and form processing. Internet address, data rate, and the location of the facility are implemented with basic form controls with default values provided for convenience and efficiency using basic XForms operations. Because different emulation scenarios will vary widely in their component structure, more complex operations are used to add and delete facilities.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

Structured representation for core elements of common clinical decision support interventions to facilitate knowledge sharing.

PubMed

Zhou, Li; Hongsermeier, Tonya; Boxwala, Aziz; Lewis, Janet; Kawamoto, Kensaku; Maviglia, Saverio; Gentile, Douglas; Teich, Jonathan M; Rocha, Roberto; Bell, Douglas; Middleton, Blackford

2013-01-01

At present, there are no widely accepted, standard approaches for representing computer-based clinical decision support (CDS) intervention types and their structural components. This study aimed to identify key requirements for the representation of five widely utilized CDS intervention types: alerts and reminders, order sets, infobuttons, documentation templates/forms, and relevant data presentation. An XML schema was proposed for representing these interventions and their core structural elements (e.g., general metadata, applicable clinical scenarios, CDS inputs, CDS outputs, and CDS logic) in a shareable manner. The schema was validated by building CDS artifacts for 22 different interventions, targeted toward guidelines and clinical conditions called for in the 2011 Meaningful Use criteria. Custom style sheets were developed to render the XML files in human-readable form. The CDS knowledge artifacts were shared via a public web portal. Our experience also identifies gaps in existing standards and informs future development of standards for CDS knowledge representation and sharing.

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

DTIC Science & Technology

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

XML — an opportunity for data standards in the geosciences

NASA Astrophysics Data System (ADS)

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.

The CMIP5 Model Documentation Questionnaire: Development of a Metadata Retrieval System for the METAFOR Common Information Model

NASA Astrophysics Data System (ADS)

Pascoe, Charlotte; Lawrence, Bryan; Moine, Marie-Pierre; Ford, Rupert; Devine, Gerry

2010-05-01

The EU METAFOR Project (http://metaforclimate.eu) has created a web-based model documentation questionnaire to collect metadata from the modelling groups that are running simulations in support of the Coupled Model Intercomparison Project - 5 (CMIP5). The CMIP5 model documentation questionnaire will retrieve information about the details of the models used, how the simulations were carried out, how the simulations conformed to the CMIP5 experiment requirements and details of the hardware used to perform the simulations. The metadata collected by the CMIP5 questionnaire will allow CMIP5 data to be compared in a scientifically meaningful way. This paper describes the life-cycle of the CMIP5 questionnaire development which starts with relatively unstructured input from domain specialists and ends with formal XML documents that comply with the METAFOR Common Information Model (CIM). Each development step is associated with a specific tool. (1) Mind maps are used to capture information requirements from domain experts and build a controlled vocabulary, (2) a python parser processes the XML files generated by the mind maps, (3) Django (python) is used to generate the dynamic structure and content of the web based questionnaire from processed xml and the METAFOR CIM, (4) Python parsers ensure that information entered into the CMIP5 questionnaire is output as CIM compliant xml, (5) CIM compliant output allows automatic information capture tools to harvest questionnaire content into databases such as the Earth System Grid (ESG) metadata catalogue. This paper will focus on how Django (python) and XML input files are used to generate the structure and content of the CMIP5 questionnaire. It will also address how the choice of development tools listed above provided a framework that enabled working scientists (who we would never ordinarily get to interact with UML and XML) to be part the iterative development process and ensure that the CMIP5 model documentation questionnaire reflects what scientists want to know about the models. Keywords: metadata, CMIP5, automatic information capture, tool development

XML: A Language To Manage the World Wide Web. ERIC Digest.

ERIC Educational Resources Information Center

Davis-Tanous, Jennifer R.

This digest provides an overview of XML (Extensible Markup Language), a markup language used to construct World Wide Web pages. Topics addressed include: (1) definition of a markup language, including comparison of XML with SGML (Standard Generalized Markup Language) and HTML (HyperText Markup Language); (2) how XML works, including sample tags,…

Context- and Template-Based Compression for Efficient Management of Data Models in Resource-Constrained Systems.

PubMed

Macho, Jorge Berzosa; Montón, Luis Gardeazabal; Rodriguez, Roberto Cortiñas

2017-08-01

The Cyber Physical Systems (CPS) paradigm is based on the deployment of interconnected heterogeneous devices and systems, so interoperability is at the heart of any CPS architecture design. In this sense, the adoption of standard and generic data formats for data representation and communication, e.g., XML or JSON, effectively addresses the interoperability problem among heterogeneous systems. Nevertheless, the verbosity of those standard data formats usually demands system resources that might suppose an overload for the resource-constrained devices that are typically deployed in CPS. In this work we present Context- and Template-based Compression (CTC), a data compression approach targeted to resource-constrained devices, which allows reducing the resources needed to transmit, store and process data models. Additionally, we provide a benchmark evaluation and comparison with current implementations of the Efficient XML Interchange (EXI) processor, which is promoted by the World Wide Web Consortium (W3C), and it is the most prominent XML compression mechanism nowadays. Interestingly, the results from the evaluation show that CTC outperforms EXI implementations in terms of memory usage and speed, keeping similar compression rates. As a conclusion, CTC is shown to be a good candidate for managing standard data model representation formats in CPS composed of resource-constrained devices.

Context- and Template-Based Compression for Efficient Management of Data Models in Resource-Constrained Systems

PubMed Central

Montón, Luis Gardeazabal

2017-01-01

The Cyber Physical Systems (CPS) paradigm is based on the deployment of interconnected heterogeneous devices and systems, so interoperability is at the heart of any CPS architecture design. In this sense, the adoption of standard and generic data formats for data representation and communication, e.g., XML or JSON, effectively addresses the interoperability problem among heterogeneous systems. Nevertheless, the verbosity of those standard data formats usually demands system resources that might suppose an overload for the resource-constrained devices that are typically deployed in CPS. In this work we present Context- and Template-based Compression (CTC), a data compression approach targeted to resource-constrained devices, which allows reducing the resources needed to transmit, store and process data models. Additionally, we provide a benchmark evaluation and comparison with current implementations of the Efficient XML Interchange (EXI) processor, which is promoted by the World Wide Web Consortium (W3C), and it is the most prominent XML compression mechanism nowadays. Interestingly, the results from the evaluation show that CTC outperforms EXI implementations in terms of memory usage and speed, keeping similar compression rates. As a conclusion, CTC is shown to be a good candidate for managing standard data model representation formats in CPS composed of resource-constrained devices. PMID:28763013

Development of clinical contents model markup language for electronic health records.

PubMed

Yun, Ji-Hyun; Ahn, Sun-Ju; Kim, Yoon

2012-09-01

To develop dedicated markup language for clinical contents models (CCM) to facilitate the active use of CCM in electronic health record systems. Based on analysis of the structure and characteristics of CCM in the clinical domain, we designed extensible markup language (XML) based CCM markup language (CCML) schema manually. CCML faithfully reflects CCM in both the syntactic and semantic aspects. As this language is based on XML, it can be expressed and processed in computer systems and can be used in a technology-neutral way. CCML HAS THE FOLLOWING STRENGTHS: it is machine-readable and highly human-readable, it does not require a dedicated parser, and it can be applied for existing electronic health record systems.

Standardized Semantic Markup for Reference Terminologies, Thesauri and Coding Systems: Benefits for distributed E-Health Applications.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Liu, Raymond; Rudolf, Dirk; Rieger, Joerg; Dudeck, Joachim

2005-01-01

With the introduction of the ICD-10 as the standard for diagnosis, the development of an electronic representation of its complete content, inherent semantics and coding rules is necessary. Our concept refers to current efforts of the CEN/TC 251 to establish a European standard for hierarchical classification systems in healthcare. We have developed an electronic representation of the ICD-10 with the extensible Markup Language (XML) that facilitates the integration in current information systems or coding software taking into account different languages and versions. In this context, XML offers a complete framework of related technologies and standard tools for processing that helps to develop interoperable applications.

Information Model Translation to Support a Wider Science Community

NASA Astrophysics Data System (ADS)

Hughes, John S.; Crichton, Daniel; Ritschel, Bernd; Hardman, Sean; Joyner, Ronald

2014-05-01

The Planetary Data System (PDS), NASA's long-term archive for solar system exploration data, has just released PDS4, a modernization of the PDS architecture, data standards, and technical infrastructure. This next generation system positions the PDS to meet the demands of the coming decade, including big data, international cooperation, distributed nodes, and multiple ways of analysing and interpreting data. It also addresses three fundamental project goals: providing more efficient data delivery by data providers to the PDS, enabling a stable, long-term usable planetary science data archive, and enabling services for the data consumer to find, access, and use the data they require in contemporary data formats. The PDS4 information architecture is used to describe all PDS data using a common model. Captured in an ontology modeling tool it supports a hierarchy of data dictionaries built to the ISO/IEC 11179 standard and is designed to increase flexibility, enable complex searches at the product level, and to promote interoperability that facilitates data sharing both nationally and internationally. A PDS4 information architecture design requirement stipulates that the content of the information model must be translatable to external data definition languages such as XML Schema, XMI/XML, and RDF/XML. To support the semantic Web standards we are now in the process of mapping the contents into RDF/XML to support SPARQL capable databases. We are also building a terminological ontology to support virtually unified data retrieval and access. This paper will provide an overview of the PDS4 information architecture focusing on its domain information model and how the translation and mapping are being accomplished.

An effective XML based name mapping mechanism within StoRM

NASA Astrophysics Data System (ADS)

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

2008-07-01

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.

Tsunami.gov: NOAA's Tsunami Information Portal

NASA Astrophysics Data System (ADS)

Shiro, B.; Carrick, J.; Hellman, S. B.; Bernard, M.; Dildine, W. P.

2014-12-01

We present the new Tsunami.gov website, which delivers a single authoritative source of tsunami information for the public and emergency management communities. The site efficiently merges information from NOAA's Tsunami Warning Centers (TWC's) by way of a comprehensive XML feed called Tsunami Event XML (TEX). The resulting unified view allows users to quickly see the latest tsunami alert status in geographic context without having to understand complex TWC areas of responsibility. The new site provides for the creation of a wide range of products beyond the traditional ASCII-based tsunami messages. The publication of modern formats such as Common Alerting Protocol (CAP) can drive geographically aware emergency alert systems like FEMA's Integrated Public Alert and Warning System (IPAWS). Supported are other popular information delivery systems, including email, text messaging, and social media updates. The Tsunami.gov portal allows NOAA staff to easily edit content and provides the facility for users to customize their viewing experience. In addition to access by the public, emergency managers and government officials may be offered the capability to log into the portal for special access rights to decision-making and administrative resources relevant to their respective tsunami warning systems. The site follows modern HTML5 responsive design practices for optimized use on mobile as well as non-mobile platforms. It meets all federal security and accessibility standards. Moving forward, we hope to expand Tsunami.gov to encompass tsunami-related content currently offered on separate websites, including the NOAA Tsunami Website, National Tsunami Hazard Mitigation Program, NOAA Center for Tsunami Research, National Geophysical Data Center's Tsunami Database, and National Data Buoy Center's DART Program. This project is part of the larger Tsunami Information Technology Modernization Project, which is consolidating the software architectures of NOAA's existing TWC's into a single system. We welcome your feedback to help Tsunami.gov become an effective public resource for tsunami information and a medium to enable better global tsunami warning coordination.

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

ERIC Educational Resources Information Center

Mitri, Michel

2012-01-01

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

Compression of Probabilistic XML Documents

NASA Astrophysics Data System (ADS)

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.

Research on Heterogeneous Data Exchange based on XML

NASA Astrophysics Data System (ADS)

Li, Huanqin; Liu, Jinfeng

Integration of multiple data sources is becoming increasingly important for enterprises that cooperate closely with their partners for e-commerce. OLAP enables analysts and decision makers fast access to various materialized views from data warehouses. However, many corporations have internal business applications deployed on different platforms. This paper introduces a model for heterogeneous data exchange based on XML. The system can exchange and share the data among the different sources. The method used to realize the heterogeneous data exchange is given in this paper.

Toxics Release Inventory Chemical Hazard Information Profiles (TRI-CHIP) Dataset

EPA Pesticide Factsheets

The Toxics Release Inventory (TRI) Chemical Hazard Information Profiles (TRI-CHIP) dataset contains hazard information about the chemicals reported in TRI. Users can use this XML-format dataset to create their own databases and hazard analyses of TRI chemicals. The hazard information is compiled from a series of authoritative sources including the Integrated Risk Information System (IRIS). The dataset is provided as a downloadable .zip file that when extracted provides XML files and schemas for the hazard information tables.

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

NASA Astrophysics Data System (ADS)

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.

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

This paper reviews the development of a web-based framework for engineering analysis. A one-dimensional, high-speed analysis code called LAPIN was used in this study, but the approach can be generalized to any engineering analysis tool. The web-based framework enables users to store, retrieve, and execute an engineering analysis from a standard web-browser. We review the encapsulation of the engineering data into the eXtensible Markup Language (XML) and various design considerations in the storage and retrieval of application data.

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

PubMed Central

Rodriguez, Nicolas; Donizelli, Marco; Le Novère, Nicolas

2007-01-01

Background The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity of the language. SBMLeditor tries to answer this need by providing a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. Results SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the editing and validation of the document. In addition to Xerces, SBMLeditor uses libSBML to check the validity and consistency of SBML files. A graphical equation editor allows an easy manipulation of MathML. SBMLeditor can be used as a module of the Systems Biology Workbench. Conclusion SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors. PMID:17341299

SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML).

PubMed

Rodriguez, Nicolas; Donizelli, Marco; Le Novère, Nicolas

2007-03-06

The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity of the language. SBMLeditor tries to answer this need by providing a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the editing and validation of the document. In addition to Xerces, SBMLeditor uses libSBML to check the validity and consistency of SBML files. A graphical equation editor allows an easy manipulation of MathML. SBMLeditor can be used as a module of the Systems Biology Workbench. SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors.

Transformation of HDF-EOS metadata from the ECS model to ISO 19115-based XML

NASA Astrophysics Data System (ADS)

Wei, Yaxing; Di, Liping; Zhao, Baohua; Liao, Guangxuan; Chen, Aijun

2007-02-01

Nowadays, geographic data, such as NASA's Earth Observation System (EOS) data, are playing an increasing role in many areas, including academic research, government decisions and even in people's every lives. As the quantity of geographic data becomes increasingly large, a major problem is how to fully make use of such data in a distributed, heterogeneous network environment. In order for a user to effectively discover and retrieve the specific information that is useful, the geographic metadata should be described and managed properly. Fortunately, the emergence of XML and Web Services technologies greatly promotes information distribution across the Internet. The research effort discussed in this paper presents a method and its implementation for transforming Hierarchical Data Format (HDF)-EOS metadata from the NASA ECS model to ISO 19115-based XML, which will be managed by the Open Geospatial Consortium (OGC) Catalogue Services—Web Profile (CSW). Using XML and international standards rather than domain-specific models to describe the metadata of those HDF-EOS data, and further using CSW to manage the metadata, can allow metadata information to be searched and interchanged more widely and easily, thus promoting the sharing of HDF-EOS data.

An Extensible "SCHEMA-LESS" Database Framework for Managing High-Throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semistructured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.; La, Tracy; Clancy, Daniel (Technical Monitor)

2002-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword searches of records for both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high throughput open database framework for managing, storing, and searching unstructured or semi structured arbitrary hierarchal models, XML and HTML.

NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

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

PubMed Central

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-based information system for planetary sciences

NASA Astrophysics Data System (ADS)

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 the resources containing the inserted values within the resources descriptions. An important facility of the IDIS search system is the multi-node search capability. This is due to the capacity of eXist to make queries on remote databases. This allows the system to show all resources which satisfy the search criteria on local node and to show how many resources are found on remote nodes, giving also a link to open the results page on remote nodes. During FP7 the development of the IDIS system will have the main goal to make the service Virtual Observatory compliant.

Development of Clinical Contents Model Markup Language for Electronic Health Records

PubMed Central

Yun, Ji-Hyun; Kim, Yoon

2012-01-01

Objectives To develop dedicated markup language for clinical contents models (CCM) to facilitate the active use of CCM in electronic health record systems. Methods Based on analysis of the structure and characteristics of CCM in the clinical domain, we designed extensible markup language (XML) based CCM markup language (CCML) schema manually. Results CCML faithfully reflects CCM in both the syntactic and semantic aspects. As this language is based on XML, it can be expressed and processed in computer systems and can be used in a technology-neutral way. Conclusions CCML has the following strengths: it is machine-readable and highly human-readable, it does not require a dedicated parser, and it can be applied for existing electronic health record systems. PMID:23115739

The Development of a Graphical User Interface Engine for the Convenient Use of the HL7 Version 2.x Interface Engine

PubMed Central

Kim, Hwa Sun; Cho, Hune

2011-01-01

Objectives The Health Level Seven Interface Engine (HL7 IE), developed by Kyungpook National University, has been employed in health information systems, however users without a background in programming have reported difficulties in using it. Therefore, we developed a graphical user interface (GUI) engine to make the use of the HL7 IE more convenient. Methods The GUI engine was directly connected with the HL7 IE to handle the HL7 version 2.x messages. Furthermore, the information exchange rules (called the mapping data), represented by a conceptual graph in the GUI engine, were transformed into program objects that were made available to the HL7 IE; the mapping data were stored as binary files for reuse. The usefulness of the GUI engine was examined through information exchange tests between an HL7 version 2.x message and a health information database system. Results Users could easily create HL7 version 2.x messages by creating a conceptual graph through the GUI engine without requiring assistance from programmers. In addition, time could be saved when creating new information exchange rules by reusing the stored mapping data. Conclusions The GUI engine was not able to incorporate information types (e.g., extensible markup language, XML) other than the HL7 version 2.x messages and the database, because it was designed exclusively for the HL7 IE protocol. However, in future work, by including additional parsers to manage XML-based information such as Continuity of Care Documents (CCD) and Continuity of Care Records (CCR), we plan to ensure that the GUI engine will be more widely accessible for the health field. PMID:22259723

The Development of a Graphical User Interface Engine for the Convenient Use of the HL7 Version 2.x Interface Engine.

PubMed

Kim, Hwa Sun; Cho, Hune; Lee, In Keun

2011-12-01

The Health Level Seven Interface Engine (HL7 IE), developed by Kyungpook National University, has been employed in health information systems, however users without a background in programming have reported difficulties in using it. Therefore, we developed a graphical user interface (GUI) engine to make the use of the HL7 IE more convenient. The GUI engine was directly connected with the HL7 IE to handle the HL7 version 2.x messages. Furthermore, the information exchange rules (called the mapping data), represented by a conceptual graph in the GUI engine, were transformed into program objects that were made available to the HL7 IE; the mapping data were stored as binary files for reuse. The usefulness of the GUI engine was examined through information exchange tests between an HL7 version 2.x message and a health information database system. Users could easily create HL7 version 2.x messages by creating a conceptual graph through the GUI engine without requiring assistance from programmers. In addition, time could be saved when creating new information exchange rules by reusing the stored mapping data. The GUI engine was not able to incorporate information types (e.g., extensible markup language, XML) other than the HL7 version 2.x messages and the database, because it was designed exclusively for the HL7 IE protocol. However, in future work, by including additional parsers to manage XML-based information such as Continuity of Care Documents (CCD) and Continuity of Care Records (CCR), we plan to ensure that the GUI engine will be more widely accessible for the health field.

Specifics on a XML Data Format for Scientific Data

NASA Astrophysics Data System (ADS)

Shaya, E.; Thomas, B.; Cheung, C.

An XML-based data format for interchange and archiving of scientific data would benefit in many ways from the features standardized in XML. Foremost of these features is the world-wide acceptance and adoption of XML. Applications, such as browsers, XQL and XSQL advanced query, XML editing, or CSS or XSLT transformation, that are coming out of industry and academia can be easily adopted and provide startling new benefits and features. We have designed a prototype of a core format for holding, in a very general way, parameters, tables, scalar and vector fields, atlases, animations and complex combinations of these. This eXtensible Data Format (XDF) makes use of XML functionalities such as: self-validation of document structure, default values for attributes, XLink hyperlinks, entity replacements, internal referencing, inheritance, and XSLT transformation. An API is available to aid in detailed assembly, extraction, and manipulation. Conversion tools to and from FITS and other existing data formats are under development. In the future, we hope to provide object oriented interfaces to C++, Java, Python, IDL, Mathematica, Maple, and various databases. http://xml.gsfc.nasa.gov/XDF

CytometryML with DICOM and FCS

NASA Astrophysics Data System (ADS)

Leif, Robert C.

2018-02-01

Abstract: Flow Cytometry Standard, FCS, and Digital Imaging and Communications in Medicine standard, DICOM, are based on extensive, superb domain knowledge, However, they are isolated systems, do not take advantage of data structures, require special programs to read and write the data, lack the capability to interoperate or work with other standards and FCS lacks many of the datatypes necessary for clinical laboratory data. The large overlap between imaging and flow cytometry provides strong evidence that both modalities should be covered by the same standard. Method: The XML Schema Definition Language, XSD 1.1 was used to translate FCS and/or DICOM objects. A MIFlowCyt file was tested with published values. Results: Previously, a significant part of an XML standard based upon a combination of FCS and DICOM has been implemented and validated with MIFlowCyt data. Strongly typed translations of FCS keywords have been constructed in XML. These keywords contain links to their DICOM and FCS equivalents.

A Priority Fuzzy Logic Extension of the XQuery Language

NASA Astrophysics Data System (ADS)

Škrbić, Srdjan; Wettayaprasit, Wiphada; Saeueng, Pannipa

2011-09-01

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

QRFXFreeze: Queryable Compressor for RFX.

PubMed

Senthilkumar, Radha; Nandagopal, Gomathi; Ronald, Daphne

2015-01-01

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

CLAIM (CLinical Accounting InforMation)--an XML-based data exchange standard for connecting electronic medical record systems to patient accounting systems.

PubMed

Guo, Jinqiu; Takada, Akira; Tanaka, Koji; Sato, Junzo; Suzuki, Muneou; Takahashi, Kiwamu; Daimon, Hiroyuki; Suzuki, Toshiaki; Nakashima, Yusei; Araki, Kenji; Yoshihara, Hiroyuki

2005-08-01

With the evolving and diverse electronic medical record (EMR) systems, there appears to be an ever greater need to link EMR systems and patient accounting systems with a standardized data exchange format. To this end, the CLinical Accounting InforMation (CLAIM) data exchange standard was developed. CLAIM is subordinate to the Medical Markup Language (MML) standard, which allows the exchange of medical data among different medical institutions. CLAIM uses eXtensible Markup Language (XML) as a meta-language. The current version, 2.1, inherited the basic structure of MML 2.x and contains two modules including information related to registration, appointment, procedure and charging. CLAIM 2.1 was implemented successfully in Japan in 2001. Consequently, it was confirmed that CLAIM could be used as an effective data exchange format between EMR systems and patient accounting systems.

The Contact Dynamics method: A nonsmooth story

NASA Astrophysics Data System (ADS)

Dubois, Frédéric; Acary, Vincent; Jean, Michel

2018-03-01

When velocity jumps are occurring, the dynamics is said to be nonsmooth. For instance, in collections of contacting rigid bodies, jumps are caused by shocks and dry friction. Without compliance at the interface, contact laws are not only non-differentiable in the usual sense but also multi-valued. Modeling contacting bodies is of interest in order to understand the behavior of numerous mechanical systems such as flexible multi-body systems, granular materials or masonry. These granular materials behave puzzlingly either like a solid or a fluid and a description in the frame of classical continuous mechanics would be welcome though far to be satisfactory nowadays. Jean-Jacques Moreau greatly contributed to convex analysis, functions of bounded variations, differential measure theory, sweeping process theory, definitive mathematical tools to deal with nonsmooth dynamics. He converted all these underlying theoretical ideas into an original nonsmooth implicit numerical method called Contact Dynamics (CD); a robust and efficient method to simulate large collections of bodies with frictional contacts and impacts. The CD method offers a very interesting complementary alternative to the family of smoothed explicit numerical methods, often called Distinct Elements Method (DEM). In this paper developments and improvements of the CD method are presented together with a critical comparative review of advantages and drawbacks of both approaches. xml:lang="fr"

Application of Architectural Patterns and Lightweight Formal Method for the Validation and Verification of Safety Critical Systems

DTIC Science & Technology

2013-09-01

to a XML file, a code that Bonine in [21] developed for a similar purpose. Using the StateRover XML log file import tool, we are able to generate a...C. Bonine , M. Shing, T.W. Otani, “Computer-aided process and tools for mobile software acquisition,” NPS, Monterey, CA, Tech. Rep. NPS-SE-13...C10P07R05– 075, 2013. [21] C. Bonine , “Specification, validation and verification of mobile application behavior,” M.S. thesis, Dept. Comp. Science, NPS

Middleware Trade Study for NASA Domain

NASA Technical Reports Server (NTRS)

Bowman, Dan

2007-01-01

This presentation presents preliminary results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are: the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL

An XML-Based Mission Command Language for Autonomous Underwater Vehicles (AUVs)

DTIC Science & Technology

2003-06-01

P. XML: How To Program . Prentice Hall, Inc. Upper Saddle River, New Jersey, 2001 Digital Signature Activity Statement, W3C www.w3.org/Signature...languages because it does not directly specify how information is to be presented, but rather defines the structure (and thus semantics) of the...command and control (C2) aspects of using XML to increase the utility of AUVs. XML programming will be addressed. Current mine warfare doctrine will be

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

PubMed

Jiang, Guoqian; Solbrig, Harold R; Chute, Christopher G

2011-01-01

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

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

PubMed

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.

"The Wonder Years" of XML.

ERIC Educational Resources Information Center

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…

A Generic Metadata Editor Supporting System Using Drupal CMS

NASA Astrophysics Data System (ADS)

Pan, J.; Banks, N. G.; Leggott, M.

2011-12-01

Metadata handling is a key factor in preserving and reusing scientific data. In recent years, standardized structural metadata has become widely used in Geoscience communities. However, there exist many different standards in Geosciences, such as the current version of the Federal Geographic Data Committee's Content Standard for Digital Geospatial Metadata (FGDC CSDGM), the Ecological Markup Language (EML), the Geography Markup Language (GML), and the emerging ISO 19115 and related standards. In addition, there are many different subsets within the Geoscience subdomain such as the Biological Profile of the FGDC (CSDGM), or for geopolitical regions, such as the European Profile or the North American Profile in the ISO standards. It is therefore desirable to have a software foundation to support metadata creation and editing for multiple standards and profiles, without re-inventing the wheels. We have developed a software module as a generic, flexible software system to do just that: to facilitate the support for multiple metadata standards and profiles. The software consists of a set of modules for the Drupal Content Management System (CMS), with minimal inter-dependencies to other Drupal modules. There are two steps in using the system's metadata functions. First, an administrator can use the system to design a user form, based on an XML schema and its instances. The form definition is named and stored in the Drupal database as a XML blob content. Second, users in an editor role can then use the persisted XML definition to render an actual metadata entry form, for creating or editing a metadata record. Behind the scenes, the form definition XML is transformed into a PHP array, which is then rendered via Drupal Form API. When the form is submitted the posted values are used to modify a metadata record. Drupal hooks can be used to perform custom processing on metadata record before and after submission. It is trivial to store the metadata record as an actual XML file or in a storage/archive system. We are working on adding many features to help editor users, such as auto completion, pre-populating of forms, partial saving, as well as automatic schema validation. In this presentation we will demonstrate a few sample editors, including an FGDC editor and a bare bone editor for ISO 19115/19139. We will also demonstrate the use of templates during the definition phase, with the support of export and import functions. Form pre-population and input validation will also be covered. Theses modules are available as open-source software from the Islandora software foundation, as a component of a larger Drupal-based data archive system. They can be easily installed as stand-alone system, or to be plugged into other existing metadata platforms.

A Petri Net-Based Software Process Model for Developing Process-Oriented Information Systems

NASA Astrophysics Data System (ADS)

Li, Yu; Oberweis, Andreas

Aiming at increasing flexibility, efficiency, effectiveness, and transparency of information processing and resource deployment in organizations to ensure customer satisfaction and high quality of products and services, process-oriented information systems (POIS) represent a promising realization form of computerized business information systems. Due to the complexity of POIS, explicit and specialized software process models are required to guide POIS development. In this chapter we characterize POIS with an architecture framework and present a Petri net-based software process model tailored for POIS development with consideration of organizational roles. As integrated parts of the software process model, we also introduce XML nets, a variant of high-level Petri nets as basic methodology for business processes modeling, and an XML net-based software toolset providing comprehensive functionalities for POIS development.

Method and system to discover and recommend interesting documents

DOEpatents

Potok, Thomas Eugene; Steed, Chad Allen; Patton, Robert Matthew

2017-01-31

Disclosed are several examples of systems that can read millions of news feeds per day about topics (e.g., your customers, competitors, markets, and partners), and provide a small set of the most relevant items to read to keep current with the overwhelming amount of information currently available. Topics of interest can be chosen by the user of the system for use as seeds. The seeds can be vectorized and compared with the target documents to determine their similarity. The similarities can be sorted from highest to lowest so that the most similar seed and target documents are at the top of the list. This output can be produced in XML format so that an RSS Reader can format the XML. This allows for easy Internet access to these recommendations.

A structured interface to the object-oriented genomics unified schema for XML-formatted data.

PubMed

Clark, Terry; Jurek, Josef; Kettler, Gregory; Preuss, Daphe

2005-01-01

Data management systems are fast becoming required components in many biology laboratories as the role of computer-based information grows. Although the need for data management systems is on the rise, their inherent complexities can deter the full and routine use of their computational capabilities. The significant undertaking to implement a capable production system can be reduced in part by adapting an established data management system. In such a way, we are leveraging the Genomics Unified Schema (GUS) developed at the Computational Biology and Informatics Laboratory at the University of Pennsylvania as a foundation for managing and analysing DNA sequence data in centromere research projects around Arabidopsis thaliana and related species. Because GUS provides a core schema that includes support for genome sequences, mRNA and its expression, and annotated chromosomes, it is ideal for synthesising a variety of parameters to analyse these repetitive and highly dynamic portions of the genome. Despite this, production-strength data management frameworks are complex, requiring dedicated efforts to adapt and maintain. The work reported in this article addresses one component of such an effort, namely the pivotal task of marshalling data from various sources into GUS. In order to harness GUS for our project, and motivated by efficiency needs, we developed a structured framework for transferring data into GUS from outside sources. This technology is embodied in a GUS object-layer processor, XMLGUS. XMLGUS facilitates incorporating data into GUS by (i) formulating an XML interface that includes relational database key constraint definitions, (ii) regularising traversal through that XML, (iii) realising automatic processing of the XML with database key constraints and (iv) allowing for special processing of input data within the framework for automated processing. The application of XMLGUS to production pipeline processing for a sequencing project and inputting the Arabidopsis genome into GUS is discussed. XMLGUS is available from the Flora website (http://flora.ittc.ku.edu/).

Modeling the Arden Syntax for medical decisions in XML.

PubMed

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.

An Expressive and Efficient Language for XML Information Retrieval.

ERIC Educational Resources Information Center

Chinenyanga, Taurai Tapiwa; Kushmerick, Nicholas

2002-01-01

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

XML Content Finally Arrives on the Web!

ERIC Educational Resources Information Center

Funke, Susan

1998-01-01

Explains extensible markup language (XML) and how it differs from hypertext markup language (HTML) and standard generalized markup language (SGML). Highlights include features of XML, including better formatting of documents, better searching capabilities, multiple uses for hyperlinking, and an increase in Web applications; Web browsers; and what…

How Does XML Help Libraries?

ERIC Educational Resources Information Center

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.…

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

PESO - The Python Based Control System of the Ondrejov 2m Telescope

NASA Astrophysics Data System (ADS)

Skoda, P.; Fuchs, J.; Honsa, J.

2005-12-01

Python has been gaining a good reputation and respectability in many areas of software development. We have chosen Python after getting the new CCD detector for the coudé spectrograph of Ondřejov observatory 2m telescope. The VersArray detector from Roper Scientific came only with the closed source library PVCAM of low-level camera control functions for Linux, so we had to write the whole astronomical data acquisition system from scratch and integrate it with the current spectrograph and telescope control systems. The final result of our effort, PESO (Python Exposure System for Ondřejov) is a highly comfortable GUI-based environment allowing the observer to change the spectrograph configuration, choose the detector acquisition mode, select the exposure parameters, and monitor the exposure progress. All of the relevant information from the control computers is written into the FITS headers by the PyFITS module, and the acquired CCD frame is immediately displayed in an SAO DS9 window using XPA calls. The GTK-based front end design was drawn in the Glade visual development tool, giving the shape and position of all widgets in single XML file, which is used in Python by a simple call of the PyGlade module. We describe our experience with the design and implementation of PESO, stressing the easiness of quick changes of the GUI, together with the capability of separate testing of every module using the Python debugger, IPython.

Get It Together: Integrating Data with XML.

ERIC Educational Resources Information Center

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.…

XML Schema Languages: Beyond DTD.

ERIC Educational Resources Information Center

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)

XML: A Publisher's Perspective.

ERIC Educational Resources Information Center

Andrews, Timothy M.

1999-01-01

Explains eXtensible Markup Language (XML) and describes how Dow Jones Interactive is using it to improve the news-gathering and dissemination process through intranets and the World Wide Web. Discusses benefits of using XML, the relationship to HyperText Markup Language (HTML), lack of available software tools and industry support, and future…

jmzML, an open-source Java API for mzML, the PSI standard for MS data.

PubMed

Côté, Richard G; Reisinger, Florian; Martens, Lennart

2010-04-01

We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

The Cadmio XML healthcare record.

PubMed

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.

NASA Constellation Distributed Simulation Middleware Trade Study

NASA Technical Reports Server (NTRS)

Hasan, David; Bowman, James D.; Fisher, Nancy; Cutts, Dannie; Cures, Edwin Z.

2008-01-01

This paper presents the results of a trade study designed to assess three distributed simulation middleware technologies for support of the NASA Constellation Distributed Space Exploration Simulation (DSES) project and Test and Verification Distributed System Integration Laboratory (DSIL). The technologies are the High Level Architecture (HLA), the Test and Training Enabling Architecture (TENA), and an XML-based variant of Distributed Interactive Simulation (DIS-XML) coupled with the Extensible Messaging and Presence Protocol (XMPP). According to the criteria and weights determined in this study, HLA scores better than the other two for DSES as well as the DSIL.

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

PubMed

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.

Towards health care process description framework: an XML DTD design.

PubMed Central

Staccini, P.; Joubert, M.; Quaranta, J. F.; Aymard, S.; Fieschi, D.; Fieschi, M.

2001-01-01

The development of health care and hospital information systems has to meet users needs as well as requirements such as the tracking of all care activities and the support of quality improvement. The use of process-oriented analysis is of-value to provide analysts with: (i) a systematic description of activities; (ii) the elicitation of the useful data to perform and record care tasks; (iii) the selection of relevant decision-making support. But paper-based tools are not a very suitable way to manage and share the documentation produced during this step. The purpose of this work is to propose a method to implement the results of process analysis according to XML techniques (eXtensible Markup Language). It is based on the IDEF0 activity modeling language (Integration DEfinition for Function modeling). A hierarchical description of a process and its components has been defined through a flat XML file with a grammar of proper metadata tags. Perspectives of this method are discussed. PMID:11825265

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

PubMed

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.

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

PubMed Central

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. PMID:12463856

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

PubMed

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 such as DICOM, SCP-ECG and aECG to support the storage of BSPMs. In summary, this research provides initial ground work for creating a complete BSPM management system.

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

Hurst, Aaron M.

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; thismore » 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.« less

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

PubMed

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.

Representing Human Expertise by the OWL Web Ontology Language to Support Knowledge Engineering in Decision Support Systems.

PubMed

Ramzan, Asia; Wang, Hai; Buckingham, Christopher

2014-01-01

Clinical decision support systems (CDSSs) often base their knowledge and advice on human expertise. Knowledge representation needs to be in a format that can be easily understood by human users as well as supporting ongoing knowledge engineering, including evolution and consistency of knowledge. This paper reports on the development of an ontology specification for managing knowledge engineering in a CDSS for assessing and managing risks associated with mental-health problems. The Galatean Risk and Safety Tool, GRiST, represents mental-health expertise in the form of a psychological model of classification. The hierarchical structure was directly represented in the machine using an XML document. Functionality of the model and knowledge management were controlled using attributes in the XML nodes, with an accompanying paper manual for specifying how end-user tools should behave when interfacing with the XML. This paper explains the advantages of using the web-ontology language, OWL, as the specification, details some of the issues and problems encountered in translating the psychological model to OWL, and shows how OWL benefits knowledge engineering. The conclusions are that OWL can have an important role in managing complex knowledge domains for systems based on human expertise without impeding the end-users' understanding of the knowledge base. The generic classification model underpinning GRiST makes it applicable to many decision domains and the accompanying OWL specification facilitates its implementation.

Adding XML to the MIS Curriculum: Lessons from the Classroom

ERIC Educational Resources Information Center

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"…

Data Manipulation in an XML-Based Digital Image Library

ERIC Educational Resources Information Center

Chang, Naicheng

2005-01-01

Purpose: To help to clarify the role of XML tools and standards in supporting transition and migration towards a fully XML-based environment for managing access to information. Design/methodology/approach: The Ching Digital Image Library, built on a three-tier architecture, is used as a source of examples to illustrate a number of methods of data…

EquiX-A Search and Query Language for XML.

ERIC Educational Resources Information Center

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

2002-01-01

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

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

PubMed Central

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.

Implementation of the Intelligent Voice System for Kazakh

NASA Astrophysics Data System (ADS)

Yessenbayev, Zh; Saparkhojayev, N.; Tibeyev, T.

2014-04-01

Modern speech technologies are highly advanced and widely used in day-to-day applications. However, this is mostly concerned with the languages of well-developed countries such as English, German, Japan, Russian, etc. As for Kazakh, the situation is less prominent and research in this field is only starting to evolve. In this research and application-oriented project, we introduce an intelligent voice system for the fast deployment of call-centers and information desks supporting Kazakh speech. The demand on such a system is obvious if the country's large size and small population is considered. The landline and cell phones become the only means of communication for the distant villages and suburbs. The system features Kazakh speech recognition and synthesis modules as well as a web-GUI for efficient dialog management. For speech recognition we use CMU Sphinx engine and for speech synthesis- MaryTTS. The web-GUI is implemented in Java enabling operators to quickly create and manage the dialogs in user-friendly graphical environment. The call routines are handled by Asterisk PBX and JBoss Application Server. The system supports such technologies and protocols as VoIP, VoiceXML, FastAGI, Java SpeechAPI and J2EE. For the speech recognition experiments we compiled and used the first Kazakh speech corpus with the utterances from 169 native speakers. The performance of the speech recognizer is 4.1% WER on isolated word recognition and 6.9% WER on clean continuous speech recognition tasks. The speech synthesis experiments include the training of male and female voices.

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

PubMed

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.

Report of Official Foreign Travel to Germany, May 16-June 1, 2001

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

J. D. Mason

2001-06-18

The Department of Energy (DOE) and associated agencies have moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ''standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardizationmore » (ISO) and the American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, I have served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During my May 2001 trip, I chaired the spring 2001 meeting of SC34 in Berlin, Germany. I also attended XML Europe 2001, a major conference on the use of SGML and XML sponsored by the Graphic Communications Association (GCA), and chaired a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there have been several past and present SGML- and XML-based projects at the Y-12 National Security Complex (Y-12). Our local project team has done SGML and XML development at Y-12 and Oak Ridge National Laboratory (ORNL) since the late 1980s. SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at Y-12 and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The ''Ferret'' system for automated classification analysis uses XML to structure its knowledge base. The Ferret team also provides XML consulting to OSTI and DOE Headquarters, particularly the National Nuclear Security Administration (NNSA). Supporting standards development allows DOE and Y-12 the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML, XML, and related topics.« less

HepML, an XML-based format for describing simulated data in high energy physics

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

2010-10-01

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces - Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size - 25.0 Kb).

A Practical Introduction to the XML, Extensible Markup Language, by Way of Some Useful Examples

ERIC Educational Resources Information Center

Snyder, Robin

2004-01-01

XML, Extensible Markup Language, is important as a way to represent and encapsulate the structure of underlying data in a portable way that supports data exchange regardless of the physical storage of the data. This paper (and session) introduces some useful and practical aspects of XML technology for sharing information in a educational setting…

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

PubMed

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

2013-04-01

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

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

PubMed

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

2017-08-18

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

Making journals accessible to the visually impaired: the future is near

PubMed Central

GARDNER, John; BULATOV, Vladimir; KELLY, Robert

2010-01-01

The American Physical Society (APS) has been a leader in using markup languages for publishing. ViewPlus has led development of innovative technologies for graphical information accessibility by people with print disabilities. APS, ViewPlus, and other collaborators in the Enhanced Reading Project are working together to develop the necessary technology and infrastructure for APS to publish its journals in the DAISY (Digital Accessible Information SYstem) eXtended Markup Language (XML) format, in which all text, math, and figures would be accessible to people who are blind or have other print disabilities. The first APS DAISY XML publications are targeted for late 2010. PMID:20676358

System for gathering and summarizing internet information

DOEpatents

Potok, Thomas E.; Elmore, Mark Thomas; Reed, Joel Wesley; Treadwell, Jim N.; Samatova, Nagiza Faridovna

2006-07-04

A computer method of gathering and summarizing large amounts of information comprises collecting information from a plurality of information sources (14, 51) according to respective maps (52) of the information sources (14), converting the collected information from a storage format to XML-language documents (26, 53) and storing the XML-language documents in a storage medium, searching for documents (55) according to a search query (13) having at least one term and identifying the documents (26) found in the search, and displaying the documents as nodes (33) of a tree structure (32) having links (34) and nodes (33) so as to indicate similarity of the documents to each other.

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

EPA Pesticide Factsheets

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

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

PubMed

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

2018-05-11

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... posting CSV file samples. Order No. 770 revised the process for filing EQRs. Pursuant to Order No. 770, one of the new processes for filing allows EQRs to be filed using an XML file. The XML schema that is needed to file EQRs in this manner is now posted on the Commission's Web site at http://www.ferc.gov/docs...

The New Online Metadata Editor for Generating Structured Metadata

NASA Astrophysics Data System (ADS)

Devarakonda, R.; Shrestha, B.; Palanisamy, G.; Hook, L.; Killeffer, T.; Boden, T.; Cook, R. B.; Zolly, L.; Hutchison, V.; Frame, M. T.; Cialella, A. T.; Lazer, K.

2014-12-01

Nobody is better suited to "describe" data than the scientist who created it. This "description" about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, and locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [1] [2]. Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. How is OME helping Big Data Centers like ORNL DAAC? The ORNL DAAC is one of NASA's Earth Observing System Data and Information System (EOSDIS) data centers managed by the ESDIS Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data. OME will allow data centers like the ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability.References:[1] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94. [2] Wilson, Bruce E., et al. "Mercury Toolset for Spatiotemporal Metadata." NASA Technical Reports Server (NTRS) (2010).

OSCAR/Surface: Metadata for the WMO Integrated Observing System WIGOS

NASA Astrophysics Data System (ADS)

Klausen, Jörg; Pröscholdt, Timo; Mannes, Jürg; Cappelletti, Lucia; Grüter, Estelle; Calpini, Bertrand; Zhang, Wenjian

2016-04-01

The World Meteorological Organization (WMO) Integrated Global Observing System (WIGOS) is a key WMO priority underpinning all WMO Programs and new initiatives such as the Global Framework for Climate Services (GFCS). It does this by better integrating WMO and co-sponsored observing systems, as well as partner networks. For this, an important aspect is the description of the observational capabilities by way of structured metadata. The 17th Congress of the Word Meteorological Organization (Cg-17) has endorsed the semantic WIGOS metadata standard (WMDS) developed by the Task Team on WIGOS Metadata (TT-WMD). The standard comprises of a set of metadata classes that are considered to be of critical importance for the interpretation of observations and the evolution of observing systems relevant to WIGOS. The WMDS serves all recognized WMO Application Areas, and its use for all internationally exchanged observational data generated by WMO Members is mandatory. The standard will be introduced in three phases between 2016 and 2020. The Observing Systems Capability Analysis and Review (OSCAR) platform operated by MeteoSwiss on behalf of WMO is the official repository of WIGOS metadata and an implementation of the WMDS. OSCAR/Surface deals with all surface-based observations from land, air and oceans, combining metadata managed by a number of complementary, more domain-specific systems (e.g., GAWSIS for the Global Atmosphere Watch, JCOMMOPS for the marine domain, the WMO Radar database). It is a modern, web-based client-server application with extended information search, filtering and mapping capabilities including a fully developed management console to add and edit observational metadata. In addition, a powerful application programming interface (API) is being developed to allow machine-to-machine metadata exchange. The API is based on an ISO/OGC-compliant XML schema for the WMDS using the Observations and Measurements (ISO19156) conceptual model. The purpose of the presentation is to acquaint the audience with OSCAR, the WMDS and the current XML schema; and, to explore the relationship to the INSPIRE XML schema. Feedback from experts in the various disciplines of meteorology, climatology, atmospheric chemistry, hydrology on the utility of the new standard and the XML schema will be solicited and will guide WMO in further evolving the WMDS.

Building Community Around Hydrologic Data Models Within CUAHSI

NASA Astrophysics Data System (ADS)

Maidment, D.

2007-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has a Hydrologic Information Systems project which aims to provide better data access and capacity for data synthesis for the nation's water information, both that collected by academic investigators and that collected by water agencies. These data include observations of streamflow, water quality, groundwater levels, weather and climate and aquatic biology. Each water agency or research investigator has a unique method of formatting their data (syntactic heterogeneity) and describing their variables (semantic heterogeneity). The result is a large agglomeration of data in many formats and descriptions whose full content is hard to interpret and analyze. CUAHSI is helping to resolve syntactic heterogeneity through the development of WaterML, a standard XML markup language for communicating water observations data through web services, and a standard relational database structure for archiving data called the Observations Data Model. Variables in these data archiving and communicating systems are indexed against a controlled vocabulary of descriptive terms to provide the capacity to synthesize common data types from disparate data sources.

XML Based Markup Languages for Specific Domains

NASA Astrophysics Data System (ADS)

Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

Educational Application of Dialogue System To Support e-Learning.

ERIC Educational Resources Information Center

Kim, Youn-Gi; Lee, Chul-Hwan; Han, Sun-Gwan

This study is on the design and implementation of an educational dialogue system to support e-learning. The learning domain to apply the dialogue system used the subject of geometry. The knowledge in the dialogue-based system for learning geometry was created and represented by XML-based AIML. The implemented system in this study can understand…

Labeling RDF Graphs for Linear Time and Space Querying

NASA Astrophysics Data System (ADS)

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.

TTCN-3 Based Conformance Testing of Mobile Broadcast Business Management System in 3G Networks

NASA Astrophysics Data System (ADS)

Wang, Zhiliang; Yin, Xia; Xiang, Yang; Zhu, Ruiping; Gao, Shirui; Wu, Xin; Liu, Shijian; Gao, Song; Zhou, Li; Li, Peng

Mobile broadcast service is one of the emerging most important new services in 3G networks. To better operate and manage mobile broadcast services, mobile broadcast business management system (MBBMS) should be designed and developed. Such a system, with its distributed nature, complicated XML data and security mechanism, faces many challenges in testing technology. In this paper, we study the conformance testing methodology of MBBMS, and design and implement a MBBMS protocol conformance testing tool based on TTCN-3, a standardized test description language that can be used in black-box testing of reactive and distributed system. In this methodology and testing tool, we present a semi-automatic XML test data generation method of TTCN-3 test suite and use HMSC model to help the design of test suite. In addition, we also propose an integrated testing method for hierarchical MBBMS security architecture. This testing tool has been used in industrial level’s testing.

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

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

Yan, Y; Mao, W; Jiang, S

2014-06-01

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.more » 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.« less

A Simple XML Producer-Consumer Protocol

NASA Technical Reports Server (NTRS)

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 performance data. These standard protocols and representations must support tasks such as profiling parallel applications, monitoring the status of computers and networks, and monitoring the performance of services provided by a computational grid. This paper describes a proposed protocol and data representation for the exchange of events in a distributed system. The protocol exchanges messages formatted in XML and it can be layered atop any low-level communication protocol such as TCP or UDP Further, we describe Java and C++ implementations of this protocol and discuss their performance. The next section will provide some further background information. Section 3 describes the main communication patterns of our protocol. Section 4 describes how we represent events and related information using XML. Section 5 describes our protocol and Section 6 discusses the performance of two implementations of the protocol. Finally, an appendix provides the XML Schema definition of our protocol and event information.

Metadata and Service at the GFZ ISDC Portal

NASA Astrophysics Data System (ADS)

Ritschel, B.

2008-05-01

The online service portal of the GFZ Potsdam Information System and Data Center (ISDC) is an access point for all manner of geoscientific geodata, its corresponding metadata, scientific documentation and software tools. At present almost 2000 national and international users and user groups have the opportunity to request Earth science data from a portfolio of 275 different products types and more than 20 Million single data files with an added volume of approximately 12 TByte. The majority of the data and information, the portal currently offers to the public, are global geomonitoring products such as satellite orbit and Earth gravity field data as well as geomagnetic and atmospheric data for the exploration. These products for Earths changing system are provided via state-of-the art retrieval techniques. The data product catalog system behind these techniques is based on the extensive usage of standardized metadata, which are describing the different geoscientific product types and data products in an uniform way. Where as all ISDC product types are specified by NASA's Directory Interchange Format (DIF), Version 9.0 Parent XML DIF metadata files, the individual data files are described by extended DIF metadata documents. Depending on the beginning of the scientific project, one part of data files are described by extended DIF, Version 6 metadata documents and the other part are specified by data Child XML DIF metadata documents. Both, the product type dependent parent DIF metadata documents and the data file dependent child DIF metadata documents are derived from a base-DIF.xsd xml schema file. The ISDC metadata philosophy defines a geoscientific product as a package consisting of mostly one or sometimes more than one data file plus one extended DIF metadata file. Because NASA's DIF metadata standard has been developed in order to specify a collection of data only, the extension of the DIF standard consists of new and specific attributes, which are necessary for an explicit identification of single data files and the set-up of a comprehensive Earth science data catalog. The huge ISDC data catalog is realized by product type dependent tables filled with data file related metadata, which have relations to corresponding metadata tables. The product type describing parent DIF XML metadata documents are stored and managed in ORACLE's XML storage structures. In order to improve the interoperability of the ISDC service portal, the existing proprietary catalog system will be extended by an ISO 19115 based web catalog service. In addition to this development there is ISDC related concerning semantic network of different kind of metadata resources, like different kind of standardized and not-standardized metadata documents and literature as well as Web 2.0 user generated information derived from tagging activities and social navigation data.

76 FR 17413 - Contract Reporting Requirements of Intrastate Natural Gas Companies; Notice of Technical Workshop...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-29

... the PDF or XML version of Form No. 549D as a method to eFile quarterly data and whether they intend on... fillable Form No. 549D PDF and XML to file data \\2\\ pursuant to Order Nos. 735 and 735-A.\\3\\ [[Page 17414... PDF ( http://www.ferc.gov/docs-filing/forms/form-549d/form-549d.pdf ) or XML ( http://www.ferc.gov...

Evaluation of Efficient XML Interchange (EXI) for Large Datasets and as an Alternative to Binary JSON Encodings

DTIC Science & Technology

2015-03-01

fall in the lossy category (Gonzalez, Woods , & Eddins, 2009, p. 420). For the textual or numeric data in XML, however, lossy compression is...7/1,337 > Professional Notes Being Efficient with Bandwidth By Lieutenant Commander Steve Debich, Lieutenant Bruce Hill, Captain Scot Miller (Retired...2005). XML Binary Characterization. Retrieved from http://www.w3.org/TR/xbc-characterization/ Gonzalez, R., Woods , R., & Eddins, S. (2009

XML Schema Guide for Primary CDR Submissions

EPA Pesticide Factsheets

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.

Using XML/HTTP to Store, Serve and Annotate Tactical Scenarios for X3D Operational Visualization and Anti-Terrorist Training

DTIC Science & Technology

2003-03-01

PXSLServlet Paul A. Open Source Relational x X 23 Tchistopolskii sql2dtd David Mertz Public domain Relational x -- sql2xml Scott Hathaway Public...March 2003. [Hunter 2001] Hunter, David ; Cagle, Kurt; Dix, Chris; Kovack, Roger; Pinnock, Jonathan, Rafter, Jeff; Beginning XML (2nd Edition...Postgraduate School Monterey, California 4. Curt Blais Naval Postgraduate School Monterey, California 5 Erik Chaum NAVSEA Undersea

New J-STAGE system accelerates digitization and distribution of academic journals from Japan

NASA Astrophysics Data System (ADS)

Sato, Ryuichi; Kubota, Soichi; Aoyama, Kota; Tsuchiya, Eri; Miyagawa, Yoshiyuki

13 years have passed since J-STAGE was launched. At present no one could deny that its user interface and functions were already out of date comparing to foreign established e-journals. So JST has developed a new system called “J-STAGE3” in order to offer better usability and give powerful dissemination of academic papers from Japan. As the result of it, they will be able to enjoy the following things: 1) integration of two databases, Journal@rchive and J-STAGE, 2) new design/interface, 3) introduction of international standard XML format, 4) advanced subscription management, 5) saving cost of publishers, and 6) improving J-STAGE online submission and review system. At the end of March 2011, we conducted a market research on current status of digitization on Japanese society journals. The report told us that digitization ratio of those was 62% in total but it was 34% in humanities/social sciences. Or it was 92% in English journals and 55% in Japanese ones. It means that we need further promotion of digitization. In this paper, we discuss functions and direction of J-STAGE3 as well as our role in promotion of digitization of Japanese society journals.

AdaFF: Adaptive Failure-Handling Framework for Composite Web Services

NASA Astrophysics Data System (ADS)

Kim, Yuna; Lee, Wan Yeon; Kim, Kyong Hoon; Kim, Jong

In this paper, we propose a novel Web service composition framework which dynamically accommodates various failure recovery requirements. In the proposed framework called Adaptive Failure-handling Framework (AdaFF), failure-handling submodules are prepared during the design of a composite service, and some of them are systematically selected and automatically combined with the composite Web service at service instantiation in accordance with the requirement of individual users. In contrast, existing frameworks cannot adapt the failure-handling behaviors to user's requirements. AdaFF rapidly delivers a composite service supporting the requirement-matched failure handling without manual development, and contributes to a flexible composite Web service design in that service architects never care about failure handling or variable requirements of users. For proof of concept, we implement a prototype system of the AdaFF, which automatically generates a composite service instance with Web Services Business Process Execution Language (WS-BPEL) according to the users' requirement specified in XML format and executes the generated instance on the ActiveBPEL engine.

CytometryML, an XML format based on DICOM and FCS for analytical cytology data.

PubMed

Leif, Robert C; Leif, Suzanne B; Leif, Stephanie H

2003-07-01

Flow Cytometry Standard (FCS) was initially created to standardize the software researchers use to analyze, transmit, and store data produced by flow cytometers and sorters. Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies. We extended the existing mapping of FCS to the Digital Imaging and Communications in Medicine (DICOM) standard to include list-mode data produced by flow cytometry, laser scanning cytometry, and microscopic image cytometry. FCS list-mode was mapped to the DICOM Waveform Information Object. We created a collection of Extensible Markup Language (XML) schemas to express the DICOM analytical cytologic text-based data types except for large binary objects. We also developed a cytometry markup language, CytometryML, in an open environment subject to continuous peer review. The feasibility of expressing the data contained in FCS, including list-mode in DICOM, was demonstrated; and a preliminary mapping for list-mode data in the form of XML schemas and documents was completed. DICOM permitted the creation of indices that can be used to rapidly locate in a list-mode file the cells that are members of a subset. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language (MathML). The use of XML format based on DICOM for analytical cytology met most of the previously specified requirements and appears capable of meeting the others; therefore, the present FCS should be retired and replaced by an open, XML-based, standard CytometryML. Copyright 2003 Wiley-Liss, Inc.

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

DTIC Science & Technology

2010-03-01

to a graphics card , and not the redesign of XML. The justification is that if XML is going to be prevalent, special optimized hardware is...the answer, similar to the specialized functions of a video card .  Given the Moore’s law that processing power doubles every few years, let the...and numerous multimedia players such as iTunes from Apple. These applications are free to use, but the source is restricted by software licenses

XML Schema Guide for Secondary CDR Submissions

EPA Pesticide Factsheets

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.

The SGML Standardization Framework and the Introduction of XML

PubMed Central

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

The SGML standardization framework and the introduction of XML.

PubMed

Fierz, W; Grütter, R

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.

XML at the ADC: Steps to a Next Generation Data Archive

NASA Astrophysics Data System (ADS)

Shaya, E.; Blackwell, J.; Gass, J.; Oliversen, N.; Schneider, G.; Thomas, B.; Cheung, C.; White, R. A.

1999-05-01

The eXtensible Markup Language (XML) is a document markup language that allows users to specify their own tags, to create hierarchical structures to qualify their data, and to support automatic checking of documents for structural validity. It is being intensively supported by nearly every major corporate software developer. Under the funds of a NASA AISRP proposal, the Astronomical Data Center (ADC, http://adc.gsfc.nasa.gov) is developing an infrastructure for importation, enhancement, and distribution of data and metadata using XML as the document markup language. We discuss the preliminary Document Type Definition (DTD, at http://adc.gsfc.nasa.gov/xml) which specifies the elements and their attributes in our metadata documents. This attempts to define both the metadata of an astronomical catalog and the `header' information of an astronomical table. In addition, we give an overview of the planned flow of data through automated pipelines from authors and journal presses into our XML archive and retrieval through the web via the XML-QL Query Language and eXtensible Style Language (XSL) scripts. When completed, the catalogs and journal tables at the ADC will be tightly hyperlinked to enhance data discovery. In addition one will be able to search on fragmentary information. For instance, one could query for a table by entering that the second author is so-and-so or that the third author is at such-and-such institution.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

CliniProteus: A flexible clinical trials information management system

PubMed Central

Mathura, Venkatarajan S; Rangareddy, Mahendiranath; Gupta, Pankaj; Mullan, Michael

2007-01-01

Clinical trials involve multi-site heterogeneous data generation with complex data input-formats and forms. The data should be captured and queried in an integrated fashion to facilitate further analysis. Electronic case-report forms (eCRF) are gaining popularity since it allows capture of clinical information in a rapid manner. We have designed and developed an XML based flexible clinical trials data management framework in .NET environment that can be used for efficient design and deployment of eCRFs to efficiently collate data and analyze information from multi-site clinical trials. The main components of our system include an XML form designer, a Patient registration eForm, reusable eForms, multiple-visit data capture and consolidated reports. A unique id is used for tracking the trial, site of occurrence, the patient and the year of recruitment. Availability http://www.rfdn.org/bioinfo/CTMS/ctms.html. PMID:21670796

Non-invasive light-weight integration engine for building EHR from autonomous distributed systems.

PubMed

Crespo Molina, Pere; Angulo Fernández, Carlos; Maldonado Segura, José A; Moner Cano, David; Robles Viejo, Montserrat

2006-01-01

Pangea-LE is a message oriented light-weight integration engine, allowing concurrent access to clinical information from disperse and heterogeneous data sources. The engine extracts the information and serves it to the requester client applications in a flexible XML format. This XML response message can be formatted on demand by the appropriate XSL (Extensible Stylesheet Language) transformation in order to fit client application needs. In this article we present a real use case sample where Pangea-LE collects and generates "on the fly" a structured view of all the patient clinical information available in a healthcare organisation. This information is presented to healthcare professionals in an EHR (Electronic Health Record) viewer Web application with patient search and EHR browsing capabilities. Implantation in a real environment has been a notable success due to the non-invasive method which extremely respects the existing information systems.

simBio: a Java package for the development of detailed cell models.

PubMed

Sarai, Nobuaki; Matsuoka, Satoshi; Noma, Akinori

2006-01-01

Quantitative dynamic computer models, which integrate a variety of molecular functions into a cell model, provide a powerful tool to create and test working hypotheses. We have developed a new modeling tool, the simBio package (freely available from ), which can be used for constructing cell models, such as cardiac cells (the Kyoto model from Matsuoka et al., 2003, 2004 a, b, the LRd model from Faber and Rudy, 2000, and the Noble 98 model from Noble et al., 1998), epithelial cells (Strieter et al., 1990) and pancreatic beta cells (Magnus and Keizer, 1998). The simBio package is written in Java, uses XML and can solve ordinary differential equations. In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models. This way of building models, through the combination of various modules, is enabled through the use of object-oriented programming concepts. Thus, simBio is a straightforward system for the creation of a variety of cell models on a common database of functional modules.

[Study of sharing platform of web-based enhanced extracorporeal counterpulsation hemodynamic waveform data].

PubMed

Huang, Mingbo; Hu, Ding; Yu, Donglan; Zheng, Zhensheng; Wang, Kuijian

2011-12-01

Enhanced extracorporeal counterpulsation (EECP) information consists of both text and hemodynamic waveform data. At present EECP text information has been successfully managed through Web browser, while the management and sharing of hemodynamic waveform data through Internet has not been solved yet. In order to manage EECP information completely, based on the in-depth analysis of EECP hemodynamic waveform file of digital imaging and communications in medicine (DICOM) format and its disadvantages in Internet sharing, we proposed the use of the extensible markup language (XML), which is currently the Internet popular data exchange standard, as the storage specification for the sharing of EECP waveform data. Then we designed a web-based sharing system of EECP hemodynamic waveform data via ASP. NET 2.0 platform. Meanwhile, we specifically introduced the four main system function modules and their implement methods, including DICOM to XML conversion module, EECP waveform data management module, retrieval and display of EECP waveform module and the security mechanism of the system.

Adaptable dialog architecture and runtime engine (AdaRTE): a framework for rapid prototyping of health dialog systems.

PubMed

Rojas-Barahona, L M; Giorgino, T

2009-04-01

Spoken dialog systems have been increasingly employed to provide ubiquitous access via telephone to information and services for the non-Internet-connected public. They have been successfully applied in the health care context; however, speech technology requires a considerable development investment. The advent of VoiceXML reduced the proliferation of incompatible dialog formalisms, at the expense of adding even more complexity. This paper introduces a novel architecture for dialogue representation and interpretation, AdaRTE, which allows developers to lay out dialog interactions through a high-level formalism, offering both declarative and procedural features. AdaRTE's aim is to provide a ground for deploying complex and adaptable dialogs whilst allowing experimentation and incremental adoption of innovative speech technologies. It enhances augmented transition networks with dynamic behavior, and drives multiple back-end realizers, including VoiceXML. It has been especially targeted to the health care context, because of the great scale and the need for reducing the barrier to a widespread adoption of dialog systems.

Integrated Design and Production Reference Integration with ArchGenXML V1.00

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

Barter, R H

2004-07-20

ArchGenXML is a tool that allows easy creation of Zope products through the use of Archetypes. The Integrated Design and Production Reference (IDPR) should be highly configurable in order to meet the needs of a diverse engineering community. Ease of configuration is key to the success of IDPR. The purpose of this paper is to describe a method of using a UML diagram editor to configure IDPR through ArchGenXML and Archetypes.

PDF for Healthcare and Child Health Data Forms.

PubMed

Zuckerman, Alan E; Schneider, Joseph H; Miller, Ken

2008-11-06

PDF-H is a new best practices standard that uses XFA forms and embedded JavaScript to combine PDF forms with XML data. Preliminary experience with AAP child health forms shows that the combination of PDF with XML is a more effective method to visualize familiar data on paper and the web than the traditional use of XML and XSLT. Both PDF-H and HL7 Clinical Document Architecture can co-exist using the same data for different display formats.

Follow the Leader Tracking by Autonomous Underwater Vehicles (AUVs) Using Acoustic Communications and Ranging

DTIC Science & Technology

2003-09-01

590-595, September 1996. Deitel , H.M., Deitel , P.J., Nieto, T.R., Lin, T.M., Sadhu, P., XML: How to Program , Prentice Hall, 2001. Du, Y...communications will result in a total track following error equal to the sum of the errors for the two vehicles........48 xv Figure 36. Test point programming ...Refer to (Hunter 2000), ( Deitel 2001), or similar references for additional information regarding the XML standard. Figure 17. XML example

Catalog Descriptions Using VOTable Files

NASA Astrophysics Data System (ADS)

Thompson, R.; Levay, K.; Kimball, T.; White, R.

2008-08-01

Additional information is frequently required to describe database table contents and make it understandable to users. For this reason, the Multimission Archive at Space Telescope (MAST) creates Òdescription filesÓ for each table/catalog. After trying various XML and CSV formats, we finally chose VOTable. These files are easy to update via an HTML form, easily read using an XML parser such as (in our case) the PHP5 SimpleXML extension, and have found multiple uses in our data access/retrieval process.

Enabling model customization and integration

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2003-09-01

Until fairly recently, the idea of dynamic model content and presentation were treated synonymously. For example, if one was to take a data flow network, which captures the dynamics of a target system in terms of the flow of data through nodal operators, then one would often standardize on rectangles and arrows for the model display. The increasing web emphasis on XML, however, suggests that the network model can have its content specified in an XML language, and then the model can be represented in a number of ways depending on the chosen style. We have developed a formal method, based on styles, that permits a model to be specified in XML and presented in 1D (text), 2D, and 3D. This method allows for customization and personalization to exert their benefits beyond e-commerce, to the area of model structures used in computer simulation. This customization leads naturally to solving the bigger problem of model integration - the act of taking models of a scene and integrating them with that scene so that there is only one unified modeling interface. This work focuses mostly on customization, but we address the integration issue in the future work section.

RUBE: an XML-based architecture for 3D process modeling and model fusion

NASA Astrophysics Data System (ADS)

Fishwick, Paul A.

2002-07-01

Information fusion is a critical problem for science and engineering. There is a need to fuse information content specified as either data or model. We frame our work in terms of fusing dynamic and geometric models, to create an immersive environment where these models can be juxtaposed in 3D, within the same interface. The method by which this is accomplished fits well into other eXtensible Markup Language (XML) approaches to fusion in general. The task of modeling lies at the heart of the human-computer interface, joining the human to the system under study through a variety of sensory modalities. I overview modeling as a key concern for the Defense Department and the Air Force, and then follow with a discussion of past, current, and future work. Past work began with a package with C and has progressed, in current work, to an implementation in XML. Our current work is defined within the RUBE architecture, which is detailed in subsequent papers devoted to key components. We have built RUBE as a next generation modeling framework using our prior software, with research opportunities in immersive 3D and tangible user interfaces.

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

NASA Astrophysics Data System (ADS)

Mansour, Essam; Höpfner, Hagen

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

Mapping DICOM to OpenDocument format

NASA Astrophysics Data System (ADS)

Yu, Cong; Yao, Zhihong

2009-02-01

In order to enhance the readability, extensibility and sharing of DICOM files, we have introduced XML into DICOM file system (SPIE Volume 5748)[1] and the multilayer tree structure into DICOM (SPIE Volume 6145)[2]. In this paper, we proposed mapping DICOM to ODF(OpenDocument Format), for it is also based on XML. As a result, the new format realizes the separation of content(including text content and image) and display style. Meanwhile, since OpenDocument files take the format of a ZIP compressed archive, the new kind of DICOM files can benefit from ZIP's lossless compression to reduce file size. Moreover, this open format can also guarantee long-term access to data without legal or technical barriers, making medical images accessible to various fields.

XML DTD and Schemas for HDF-EOS

NASA Technical Reports Server (NTRS)

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.

MedlinePlus Milestones: 1998-present

MedlinePlus

... page links and information daily and also offers access to this full XML content through its Web ... search-based Web service that allows developers to access MedlinePlus health topic data in XML format. MedlinePlus ...

ForConX: A forcefield conversion tool based on XML.

PubMed

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.

AdaRTE: adaptable dialogue architecture and runtime engine. A new architecture for health-care dialogue systems.

PubMed

Rojas-Barahona, L M; Giorgino, T

2007-01-01

Spoken dialogue systems have been increasingly employed to provide ubiquitous automated access via telephone to information and services for the non-Internet-connected public. In the health care context, dialogue systems have been successfully applied. Nevertheless, speech-based technology is not easy to implement because it requires a considerable development investment. The advent of VoiceXML for voice applications contributed to reduce the proliferation of incompatible dialogue interpreters, but introduced new complexity. As a response to these issues, we designed an architecture for dialogue representation and interpretation, AdaRTE, which allows developers to layout dialogue interactions through a high level formalism that offers both declarative and procedural features. AdaRTE aim is to provide a ground for deploying complex and adaptable dialogues whilst allows the experimentation and incremental adoption of innovative speech technologies. It provides the dynamic behavior of Augmented Transition Networks and enables the generation of different backends formats such as VoiceXML. It is especially targeted to the health care context, where a framework for easy dialogue deployment could reduce the barrier for a more widespread adoption of dialogue systems.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

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

Tongue Scrapers Only Slightly Reduce Bad Breath

MedlinePlus

... information you need from the Academy of General Dentistry Friday, June 29, 2018 About | Contact InfoBites Quick ... study in the September/October issue of General Dentistry, the Academy?xml:namespace> of General Dentistry?xml: ...

XML in an Adaptive Framework for Instrument Control

NASA Technical Reports Server (NTRS)

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.

XML Technology Assessment

DTIC Science & Technology

2001-01-01

System (GCCS) Track Database Management System (TDBM) (3) GCCS Integrated Imagery and Intelligence (3) Intelligence Shared Data Server (ISDS) General ...The CTH is a powerful model that will allow more than just message systems to exchange information. It could be used for object-oriented databases, as...of the Naval Integrated Tactical Environmental System I (NITES I) is used as a case study to demonstrate the utility of this distributed component

20 CFR 619.4 - Data exchange standardization for the UI Benefits and Tax Systems.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Benefits and Tax Systems. 619.4 Section 619.4 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION... § 619.4 Data exchange standardization for the UI Benefits and Tax Systems. (a) XML is the data exchange standard for the real time ICON applications set out in § 619.2 and for the SIDES exchanges set out in...

A collaborative computer auditing system under SOA-based conceptual model

NASA Astrophysics Data System (ADS)

Cong, Qiushi; Huang, Zuoming; Hu, Jibing

2013-03-01

Some of the current challenges of computer auditing are the obstacles to retrieving, converting and translating data from different database schema. During the last few years, there are many data exchange standards under continuous development such as Extensible Business Reporting Language (XBRL). These XML document standards can be used for data exchange among companies, financial institutions, and audit firms. However, for many companies, it is still expensive and time-consuming to translate and provide XML messages with commercial application packages, because it is complicated and laborious to search and transform data from thousands of tables in the ERP databases. How to transfer transaction documents for supporting continuous auditing or real time auditing between audit firms and their client companies is a important topic. In this paper, a collaborative computer auditing system under SOA-based conceptual model is proposed. By utilizing the widely used XML document standards and existing data transformation applications developed by different companies and software venders, we can wrap these application as commercial web services that will be easy implemented under the forthcoming application environments: service-oriented architecture (SOA). Under the SOA environments, the multiagency mechanism will help the maturity and popularity of data assurance service over the Internet. By the wrapping of data transformation components with heterogeneous databases or platforms, it will create new component markets composed by many software vendors and assurance service companies to provide data assurance services for audit firms, regulators or third parties.

Common Data Format: New XML and Conversion Tools

NASA Astrophysics Data System (ADS)

Han, D. B.; Liu, M. H.; McGuire, R. E.

2002-12-01

Common Data Format (CDF) is a self-describing platform-independent data format for storing, accessing, and manipulating scalar and multidimensional scientific data sets. Significant benefit has accrued to specific science communities from their use of standard formats within those communities. Examples include the International Solar Terrestrial Physics (ISTP) community in using CDF for traditional space physics data (fields, particles and plasma, waves, and images), the worldwide astronomical community in using FITS (Flexible Image Transport System) for solar data (primarily spectral images), the NASA Planetary community in using Planetary Data System (PDS) Labels, and the earth science community in using Hierarchical Data Format (HDF). Scientific progress in solar-terrestrial physics continues to be impeded by the multiplicity of available standards for data formats and dearth of general data format translators. As a result, scientists today spend a significant amount of time translating data into the format they are familiar with for their research. To minimize this unnecessary data translation time and to allow more research time, the CDF office located at GSFC National Space Science Data Center (NSSDC) has developed HDF-to-CDF and FITS-to-CDF translators, and employed the eXtensible Markup Language (XML) technology to facilitate and promote data interoperability within the space science community. We will present the current status of the CDF work including the conversion tools that have been recently developed, conversion tools that are planned in the near future, share some of the XML experiences, and use the discussion to gain community feedback to our planned future work.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

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

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

Suggestions for Improvement of User Access to GOCE L2 Data

NASA Astrophysics Data System (ADS)

Tscherning, C. C.

2011-07-01

ESA's has required that most GOCE L2 products are delivered in XML format. This creates difficulties for the users because a Parser written in Perl is needed to convert the files to files without XML tags. However several products, such as the coefficients of spherical harmonic coefficients are made available on standard form through the International Center for Global Gravity Field Models. The variance-covariance information for the gravity field models is only available without XML tags. It is suggested that all XML products are made available in the Virtual Data Archive as files without tags. This will besides making the data directly usable by a FORTRAN program also reduce the size (storage requirements) of the product to about 30 %. A further reduction of used storage should be made by tuning the number of digits for the individual quantities in the products, so that it corresponds to the actual number of significant digits.

An XML-based method for astronomy software designing

NASA Astrophysics Data System (ADS)

Liao, Mingxue; Aili, Yusupu; Zhang, Jin

XML-based method for standardization of software designing is introduced and analyzed and successfully applied to renovating the hardware and software of the digital clock at Urumqi Astronomical Station. Basic strategy for eliciting time information from the new digital clock of FT206 in the antenna control program is introduced. By FT206, the need to compute how many centuries passed since a certain day with sophisticated formulas is eliminated and it is no longer necessary to set right UT time for the computer holding control over antenna because the information about year, month, day are all deduced from Julian day dwelling in FT206, rather than from computer time. With XML-based method and standard for software designing, various existing designing methods are unified, communications and collaborations between developers are facilitated, and thus Internet-based mode of developing software becomes possible. The trend of development of XML-based designing method is predicted.

Utilizing the Structure and Content Information for XML Document Clustering

NASA Astrophysics Data System (ADS)

Tran, Tien; Kutty, Sangeetha; Nayak, Richi

This paper reports on the experiments and results of a clustering approach used in the INEX 2008 document mining challenge. The clustering approach utilizes both the structure and content information of the Wikipedia XML document collection. A latent semantic kernel (LSK) is used to measure the semantic similarity between XML documents based on their content features. The construction of a latent semantic kernel involves the computing of singular vector decomposition (SVD). On a large feature space matrix, the computation of SVD is very expensive in terms of time and memory requirements. Thus in this clustering approach, the dimension of the document space of a term-document matrix is reduced before performing SVD. The document space reduction is based on the common structural information of the Wikipedia XML document collection. The proposed clustering approach has shown to be effective on the Wikipedia collection in the INEX 2008 document mining challenge.

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

NASA Astrophysics Data System (ADS)

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

2000-10-01

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

Automating Data Submission to a National Archive

NASA Astrophysics Data System (ADS)

Work, T. T.; Chandler, C. L.; Groman, R. C.; Allison, M. D.; Gegg, S. R.; Biological; Chemical Oceanography Data Management Office

2010-12-01

In late 2006, the U.S. National Science Foundation (NSF) funded the Biological and Chemical Oceanographic Data Management Office (BCO-DMO) at Woods Hole Oceanographic Institution (WHOI) to work closely with investigators to manage oceanographic data generated from their research projects. One of the final data management tasks is to ensure that the data are permanently archived at the U.S. National Oceanographic Data Center (NODC) or other appropriate national archiving facility. In the past, BCO-DMO submitted data to NODC as an email with attachments including a PDF file (a manually completed metadata record) and one or more data files. This method is no longer feasible given the rate at which data sets are contributed to BCO-DMO. Working with collaborators at NODC, a more streamlined and automated workflow was developed to keep up with the increased volume of data that must be archived at NODC. We will describe our new workflow; a semi-automated approach for contributing data to NODC that includes a Federal Geographic Data Committee (FGDC) compliant Extensible Markup Language (XML) metadata file accompanied by comma-delimited data files. The FGDC XML file is populated from information stored in a MySQL database. A crosswalk described by an Extensible Stylesheet Language Transformation (XSLT) is used to transform the XML formatted MySQL result set to a FGDC compliant XML metadata file. To ensure data integrity, the MD5 algorithm is used to generate a checksum and manifest of the files submitted to NODC for permanent archive. The revised system supports preparation of detailed, standards-compliant metadata that facilitate data sharing and enable accurate reuse of multidisciplinary information. The approach is generic enough to be adapted for use by other data management groups.

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

NASA Technical Reports Server (NTRS)

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.

Implementation and transition of data interchange for geotechnical and geoenvironmental specialists (DIGGS v2.0).

DOT National Transportation Integrated Search

2017-01-01

Data Interchange for Geotechnical and Geoenvironmental Specialists (DIGGS) is an XML-based system : developed under a Federal Highway Administration (FHWA) State Pooled Funding Study led by the : Ohio Department of Transportation (ODOT) from 2005 to ...

Design and implementation of a health data interoperability mediator.

PubMed

Kuo, Mu-Hsing; Kushniruk, Andre William; Borycki, Elizabeth Marie

2010-01-01

The objective of this study is to design and implement a common-gateway oriented mediator to solve the health data interoperability problems that exist among heterogeneous health information systems. The proposed mediator has three main components: (1) a Synonym Dictionary (SD) that stores a set of global metadata and terminologies to serve as the mapping intermediary, (2) a Semantic Mapping Engine (SME) that can be used to map metadata and instance semantics, and (3) a DB-to-XML module that translates source health data stored in a database into XML format and back. A routine admission notification data exchange scenario is used to test the efficiency and feasibility of the proposed mediator. The study results show that the proposed mediator can make health information exchange more efficient.

Are We Ready for Another Change? Digital Signatures Can Change How We Handle the Academic Record

ERIC Educational Resources Information Center

Black, Thomas C.; Mohr, John

2004-01-01

In this electronic age, where information is digital and service is virtual, the registrar profession is changing rapidly to keep up with increasing standards and expectations. EDI and now XML standards enable system-to-system exchanges of academic records information. While many of the registrar's profession display student academic records under…

The XML approach to implementing space link extension service management

NASA Technical Reports Server (NTRS)

Tai, W.; Welz, G. A.; Theis, G.; Yamada, T.

2001-01-01

A feasibility study has been conducted at JPL, ESOC, and ISAS to assess the possible applications of the eXtensible Mark-up Language (XML) capabilities to the implementation of the CCSDS Space Link Extension (SLE) Service Management function.

XTCE. XML Telemetry and Command Exchange Tutorial

NASA Technical Reports Server (NTRS)

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.

XML Schema Versioning Policies Version 1.0

NASA Astrophysics Data System (ADS)

Harrison, Paul; Demleitner, Markus; Major, Brian; Dowler, Pat; Harrison, Paul

2018-05-01

This note describes the recommended practice for the evolution of IVOA standard XML schemata that are associated with IVOA standards. The criteria for deciding what might be considered major and minor changes and the policies for dealing with each case are described.

The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides

PubMed Central

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

2011-01-01

Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data. PMID:21572508

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

PubMed

Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

2006-11-01

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

The Graphical Representation of the Digital Astronaut Physiology Backbone

NASA Technical Reports Server (NTRS)

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.

A Customizable Importer for the Clinical Data Warehouses PaDaWaN and I2B2.

PubMed

Fette, Georg; Kaspar, Mathias; Dietrich, Georg; Ertl, Maximilian; Krebs, Jonathan; Stoerk, Stefan; Puppe, Frank

2017-01-01

In recent years, clinical data warehouses (CDW) storing routine patient data have become more and more popular to support scientific work in the medical domain. Although CDW systems provide interfaces to import new data, these interfaces have to be used by processing tools that are often not included in the systems themselves. In order to establish an extraction-transformation-load (ETL) workflow, already existing components have to be taken or new components have to be developed to perform the load part of the ETL. We present a customizable importer for the two CDW systems PaDaWaN and I2B2, which is able to import the most common import formats (plain text, CSV and XML files). In order to be run, the importer only needs a configuration file with the user credentials for the target CDW and a list of XML import configuration files, which determine how already exported data is indented to be imported. The importer is provided as a Java program, which has no further software requirements.

Infrastructural considerations for supporting POC devices. Healthcare executives must focus on creating integration-friendly environments for the most effective use of mobile devices.

PubMed

Hashem, Ahmad; Ruggeri, Roberto

2003-01-01

Creating an integration-friendly infrastructure is the best way to prepare for current as well as next-generation POC devices. Fortunately, hassle-free system integration is needed throughout healthcare today for reasons beyond the domain of POC devices, so integration progress already made in other areas helps pave the way for POC devices. Healthcare IT professionals, as much or more than any other IT group, have had to deal with the challenges of integrating disparate systems. When considering deployment of POC devices, you will want to make sure they adhere to open industry standards. In this way, these important devices won't add to the problem of disparate systems, but will contribute to the solution. We see XML and Web services as being especially important to the future of healthcare delivery and administration. XML and Web services, along with powerful orchestrators, can provide an ever-richer collection of clinical data to be delivered to, and received from, the POC devices that will become an ever more important addition to the physician armamentarium.

Home Performance XML to Real Estate Standards Organization Data Dictionary Translator

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

2015-10-27

This translator takes fields from the HPXML and translates them into RESO’s Data Dictionary, which is used in MLS systems for real estate transactions across the country. The purpose is to get energy efficiency data into the real estate transaction.

Enabling knowledge discovery: taxonomy development for NASA

NASA Technical Reports Server (NTRS)

Dutra, J.; Busch, J.

2003-01-01

This white paper provides the background for why it is important to take the next steps with the NASA taxonomy including test and validation, XML schema development, integration with the FirstGov federal search engine, the OneNASA portal and its supporting web content management system.

The version control service for the ATLAS data acquisition configuration files

NASA Astrophysics Data System (ADS)

Soloviev, Igor

2012-12-01

The ATLAS experiment at the LHC in Geneva uses a complex and highly distributed Trigger and Data Acquisition system, involving a very large number of computing nodes and custom modules. The configuration of the system is specified by schema and data in more than 1000 XML files, with various experts responsible for updating the files associated with their components. Maintaining an error free and consistent set of XML files proved a major challenge. Therefore a special service was implemented; to validate any modifications; to check the authorization of anyone trying to modify a file; to record who had made changes, plus when and why; and to provide tools to compare different versions of files and to go back to earlier versions if required. This paper provides details of the implementation and exploitation experience, that may be interesting for other applications using many human-readable files maintained by different people, where consistency of the files and traceability of modifications are key requirements.

Evaluation of ISO EN 13606 as a result of its implementation in XML

PubMed Central

Sun, Shanghua; Hassan, Taher; Kalra, Dipak

2013-01-01

The five parts of the ISO EN 13606 standard define a means by which health-care records can be exchanged between computer systems. Starting within the European standardisation process, it has now become internationally ratified in ISO. However, ISO standards do not require that a reference implementation be provided, and in order for ISO EN 13606 to deliver the expected benefits, it must be provided not as a document, but as an operational system that is not vendor specific. This article describes the evolution of an Extensible Markup Language (XML) Schema through three iterations, each of which emphasised one particular approach to delivering an executable equivalent to the printed standard. Developing these operational versions and incorporating feedback from users of these demonstrated where implementation compromises were needed and exposed defects in the standard. These are discussed herein. They may require a future technical revision to ISO EN 13606 to resolve the issues identified. PMID:23995217

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

XML: An Introduction.

ERIC Educational Resources Information Center

Lewis, John D.

1998-01-01

Describes XML (extensible markup language), a new language classification submitted to the World Wide Web Consortium that is defined in terms of both SGML (Standard Generalized Markup Language) and HTML (Hypertext Markup Language), specifically designed for the Internet. Limitations of PDF (Portable Document Format) files for electronic journals…

Integration of M&S (Modeling and Simulation), Software Design and DoDAF (Department of Defense Architecture Framework (RT 24)

DTIC Science & Technology

2012-04-09

between BPMN , SysML, and Arena ........................................... 16 Capabilities, Activities, Resources, Performers...Proof of Concept ................................................................ 22 BPMN 2.0 XML to Arena Converter...21 Figure 5: BPMN 2.0 XML StartEvent (Excerpt

The PDS-based Data Processing, Archiving and Management Procedures in Chang'e Mission

NASA Astrophysics Data System (ADS)

Zhang, Z. B.; Li, C.; Zhang, H.; Zhang, P.; Chen, W.

2017-12-01

PDS is adopted as standard format of scientific data and foundation of all data-related procedures in Chang'e mission. Unlike the geographically distributed nature of the planetary data system, all procedures of data processing, archiving, management and distribution are proceeded in the headquarter of Ground Research and Application System of Chang'e mission in a centralized manner. The RAW data acquired by the ground stations is transmitted to and processed by data preprocessing subsystem (DPS) for the production of PDS-compliant Level 0 Level 2 data products using established algorithms, with each product file being well described using an attached label, then all products with the same orbit number are put together into a scheduled task for archiving along with a XML archive list file recoding all product files' properties such as file name, file size etc. After receiving the archive request from DPS, data management subsystem (DMS) is provoked to parse the XML list file to validate all the claimed files and their compliance to PDS using a prebuilt data dictionary, then to exact metadata of each data product file from its PDS label and the fields of its normalized filename. Various requirements of data management, retrieving, distribution and application can be well met using the flexible combination of the rich metadata empowered by the PDS. In the forthcoming CE-5 mission, all the design of data structure and procedures will be updated from PDS version 3 used in previous CE-1, CE-2 and CE-3 missions to the new version 4, the main changes would be: 1) a dedicated detached XML label will be used to describe the corresponding scientific data acquired by the 4 instruments carried, the XML parsing framework used in archive list validation will be reused for the label after some necessary adjustments; 2) all the image data acquired by the panorama camera, landing camera and lunar mineralogical spectrometer should use an Array_2D_Image/Array_3D_Image object to store image data, and use a Table_Character object to store image frame header; the tabulated data acquired by the lunar regolith penetrating radar should use a Table_Binary object to store measurements.

National Space Science Data Center Information Model

NASA Astrophysics Data System (ADS)

Bell, E. V.; McCaslin, P.; Grayzeck, E.; McLaughlin, S. A.; Kodis, J. M.; Morgan, T. H.; Williams, D. R.; Russell, J. L.

2013-12-01

The National Space Science Data Center (NSSDC) was established by NASA in 1964 to provide for the preservation and dissemination of scientific data from NASA missions. It has evolved to support distributed, active archives that were established in the Planetary, Astrophysics, and Heliophysics disciplines through a series of Memoranda of Understanding. The disciplines took over responsibility for working with new projects to acquire and distribute data for community researchers while the NSSDC remained vital as a deep archive. Since 2000, NSSDC has been using the Archive Information Package to preserve data over the long term. As part of its effort to streamline the ingest of data into the deep archive, the NSSDC developed and implemented a data model of desired and required metadata in XML. This process, in use for roughly five years now, has been successfully used to support the identification and ingest of data into the NSSDC archive, most notably those data from the Planetary Data System (PDS) submitted under PDS3. A series of software packages (X-ware) were developed to handle the submission of data from the PDS nodes utilizing a volume structure. An XML submission manifest is generated at the PDS provider site prior to delivery to NSSDC. The manifest ensures the fidelity of PDS data delivered to NSSDC. Preservation metadata is captured in an XML object when NSSDC archives the data. With the recent adoption by the PDS of the XML-based PDS4 data model, there is an opportunity for the NSSDC to provide additional services to the PDS such as the preservation, tracking, and restoration of individual products (e.g., a specific data file or document), which was unfeasible in the previous PDS3 system. The NSSDC is modifying and further streamlining its data ingest process to take advantage of the PDS4 model, an important consideration given the ever-increasing amount of data being generated and archived by orbiting missions at the Moon and Mars, other active projects such as BRRISON, LADEE, MAVEN, INSIGHT, OSIRIS-REX and ground-based observatories. Streamlining the ingest process also benefits the continued processing of PDS3 data. We will report on our progress and status.

Castles Made of Sand: Building Sustainable Digitized Collections Using XML.

ERIC Educational Resources Information Center

Ragon, Bart

2003-01-01

Describes work at the University of Virginia library to digitize special collections. Discusses the use of XML (Extensible Markup Language); providing access to original source materials; DTD (Document Type Definition); TEI (Text Encoding Initiative); metadata; XSL (Extensible Style Language); and future possibilities. (LRW)

Chemical markup, XML and the World-Wide Web. 3. Toward a signed semantic chemical web of trust.

PubMed

Gkoutos, G V; Murray-Rust, P; Rzepa, H S; Wright, M

2001-01-01

We describe how a collection of documents expressed in XML-conforming languages such as CML and XHTML can be authenticated and validated against digital signatures which make use of established X.509 certificate technology. These can be associated either with specific nodes in the XML document or with the entire document. We illustrate this with two examples. An entire journal article expressed in XML has its individual components digitally signed by separate authors, and the collection is placed in an envelope and again signed. The second example involves using a software robot agent to acquire a collection of documents from a specified URL, to perform various operations and transformations on the content, including expressing molecules in CML, and to automatically sign the various components and deposit the result in a repository. We argue that these operations can used as components for building what we term an authenticated and semantic chemical web of trust.

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

PubMed

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.

XML Translator for Interface Descriptions

NASA Technical Reports Server (NTRS)

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.

US National Geothermal Data System: Web feature services and system operations

NASA Astrophysics Data System (ADS)

Richard, Stephen; Clark, Ryan; Allison, M. Lee; Anderson, Arlene

2013-04-01

The US National Geothermal Data System is being developed with support from the US Department of Energy to reduce risk in geothermal energy development by providing online access to the body of geothermal data available in the US. The system is being implemented using Open Geospatial Consortium web services for catalog search (CSW), map browsing (WMS), and data access (WFS). The catalog now includes 2427 registered resources, mostly individual documents accessible via URL. 173 WMS and WFS services are registered, hosted by 4 NGDS system nodes, as well as 6 other state geological surveys. Simple feature schema for interchange formats have been developed by an informal community process in which draft content models are developed based on the information actually available in most data provider's internal datasets. A template pattern is used for the content models so that commonly used content items have the same name and data type across models. Models are documented in Excel workbooks and posted for community review with a deadline for comment; at the end of the comment period a technical working group reviews and discusses comments and votes on adoption. When adopted, an XML schema is implemented for the content model. Our approach has been to keep the focus of each interchange schema narrow, such that simple-feature (flat file) XML schema are sufficient to implement the content model. Keeping individual interchange formats simple, and allowing flexibility to introduce new content models as needed have both assisted in adoption of the service architecture. One problem that remains to be solved is that off-the-shelf server packages (GeoServer, ArcGIS server) do not permit configuration of a normative schema location to be bound with XML namespaces in instance documents. Such configuration is possible with GeoServer using a more complex deployment process. XML interchange format schema versions are indicated by the namespace URI; because of the schema location problems, namespace URIs are redirected to the normative schema location. An additional issue that needs consideration is the expected lifetime of a service instance. A service contract should be accessible online and discoverable as part of the metadata for each service instance; this contract should specify the policy for service termination process--e.g. how notification will be made, if there is an expected end-of-life date. Application developers must be aware of these lifetime limitations to avoid unexpected failures. The evolution of the the service inventory to date has been driven primarily by data providers wishing to improve access to their data holdings. Focus is currently shifting towards improving tools for data consumer interaction--search, data inspection, and download. Long term viability of the system depends on business interdependence between the data providers and data consumers.

PACS and electronic health records

NASA Astrophysics Data System (ADS)

Cohen, Simona; Gilboa, Flora; Shani, Uri

2002-05-01

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

Timely Diagnostic Feedback for Database Concept Learning

ERIC Educational Resources Information Center

Lin, Jian-Wei; Lai, Yuan-Cheng; Chuang, Yuh-Shy

2013-01-01

To efficiently learn database concepts, this work adopts association rules to provide diagnostic feedback for drawing an Entity-Relationship Diagram (ERD). Using association rules and Asynchronous JavaScript and XML (AJAX) techniques, this work implements a novel Web-based Timely Diagnosis System (WTDS), which provides timely diagnostic feedback…

Distributed Learning Metadata Standards

ERIC Educational Resources Information Center

McClelland, Marilyn

2004-01-01

Significant economies can be achieved in distributed learning systems architected with a focus on interoperability and reuse. The key building blocks of an efficient distributed learning architecture are the use of standards and XML technologies. The goal of plug and play capability among various components of a distributed learning system…

Applying Data Mining Principles to Library Data Collection.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

Explains how libraries can use data mining techniques for more effective data collection. Highlights include three phases: data selection and acquisition; data preparation and processing, including a discussion of the use of XML (extensible markup language); and data interpretation and integration, including database management systems. (LRW)

voevent-parse: Parse, manipulate, and generate VOEvent XML packets

NASA Astrophysics Data System (ADS)

Staley, Tim D.

2014-11-01

voevent-parse, written in Python, parses, manipulates, and generates VOEvent XML packets; it is built atop lxml.objectify. Details of transients detected by many projects, including Fermi, Swift, and the Catalina Sky Survey, are currently made available as VOEvents, which is also the standard alert format by future facilities such as LSST and SKA. However, working with XML and adhering to the sometimes lengthy VOEvent schema can be a tricky process. voevent-parse provides convenience routines for common tasks, while allowing the user to utilise the full power of the lxml library when required. An earlier version of voevent-parse was part of the pysovo (ascl:1411.002) library.

The Surgical Simulation and Training Markup Language (SSTML): an XML-based language for medical simulation.

PubMed

Bacon, James; Tardella, Neil; Pratt, Janey; Hu, John; English, James

2006-01-01

Under contract with the Telemedicine & Advanced Technology Research Center (TATRC), Energid Technologies is developing a new XML-based language for describing surgical training exercises, the Surgical Simulation and Training Markup Language (SSTML). SSTML must represent everything from organ models (including tissue properties) to surgical procedures. SSTML is an open language (i.e., freely downloadable) that defines surgical training data through an XML schema. This article focuses on the data representation of the surgical procedures and organ modeling, as they highlight the need for a standard language and illustrate the features of SSTML. Integration of SSTML with software is also discussed.

Specification, Design, and Analysis of Advanced HUMS Architectures

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

2004-01-01

During the two-year project period, we have worked on several aspects of domain-specific architectures for HUMS. In particular, we looked at using scenario-based approach for the design and designed a language for describing such architectures. The language is now being used in all aspects of our HUMS design. In particular, we have made contributions in the following areas. 1) We have employed scenarios in the development of HUMS in three main areas. They are: (a) To improve reusability by using scenarios as a library indexing tool and as a domain analysis tool; (b) To improve maintainability by recording design rationales from two perspectives - problem domain and solution domain; (c) To evaluate the software architecture. 2) We have defined a new architectural language called HADL or HUMS Architectural Definition Language. It is a customized version of xArch/xADL. It is based on XML and, hence, is easily portable from domain to domain, application to application, and machine to machine. Specifications written in HADL can be easily read and parsed using the currently available XML parsers. Thus, there is no need to develop a plethora of software to support HADL. 3) We have developed an automated design process that involves two main techniques: (a) Selection of solutions from a large space of designs; (b) Synthesis of designs. However, the automation process is not an absolute Artificial Intelligence (AI) approach though it uses a knowledge-based system that epitomizes a specific HUMS domain. The process uses a database of solutions as an aid to solve the problems rather than creating a new design in the literal sense. Since searching is adopted as the main technique, the challenges involved are: (a) To minimize the effort in searching the database where a very large number of possibilities exist; (b) To develop representations that could conveniently allow us to depict design knowledge evolved over many years; (c) To capture the required information that aid the automation process.

Design and implementation of a portal for the medical equipment market: MEDICOM.

PubMed

Palamas, S; Kalivas, D; Panou-Diamandi, O; Zeelenberg, C; van Nimwegen, C

2001-01-01

The MEDICOM (Medical Products Electronic Commerce) Portal provides the electronic means for medical-equipment manufacturers to communicate online with their customers while supporting the Purchasing Process and Post Market Surveillance. The Portal offers a powerful Internet-based search tool for finding medical products and manufacturers. Its main advantage is the fast, reliable and up-to-date retrieval of information while eliminating all unrelated content that a general-purpose search engine would retrieve. The Universal Medical Device Nomenclature System (UMDNS) registers all products. The Portal accepts end-user requests and generates a list of results containing text descriptions of devices, UMDNS attribute values, and links to manufacturer Web pages and online catalogues for access to more-detailed information. Device short descriptions are provided by the corresponding manufacturer. The Portal offers technical support for integration of the manufacturers Web sites with itself. The network of the Portal and the connected manufacturers sites is called the MEDICOM system. To establish an environment hosting all the interactions of consumers (health care organizations and professionals) and providers (manufacturers, distributors, and resellers of medical devices). The Portal provides the end-user interface, implements system management, and supports database compatibility. The Portal hosts information about the whole MEDICOM system (Common Database) and summarized descriptions of medical devices (Short Description Database); the manufacturers servers present extended descriptions. The Portal provides end-user profiling and registration, an efficient product-searching mechanism, bulletin boards, links to on-line libraries and standards, on-line information for the MEDICOM system, and special messages or advertisements from manufacturers. Platform independence and interoperability characterize the system design. Relational Database Management Systems are used for the system s databases. The end-user interface is implemented using HTML, Javascript, Java applets, and XML documents. Communication between the Portal and the manufacturers servers is implemented using a CORBA interface. Remote administration of the Portal is enabled by dynamically-generated HTML interfaces based on XML documents. A representative group of users evaluated the system. The aim of the evaluation was validation of the usability of all of MEDICOM s functionality. The evaluation procedure was based on ISO/IEC 9126 Information technology - Software product evaluation - Quality characteristics and guidelines for their use. The overall user evaluation of the MEDICOM system was very positive. The MEDICOM system was characterized as an innovative concept that brings significant added value to medical-equipment commerce. The eventual benefits of the MEDICOM system are (a) establishment of a worldwide-accessible marketplace between manufacturers and health care professionals that provides up-to-date and high-quality product information in an easy and friendly way and (b) enhancement of the efficiency of marketing procedures and after-sales support.

Design and Implementation of a Portal for the Medical Equipment Market: MEDICOM

PubMed Central

Kalivas, Dimitris; Panou-Diamandi, Ourania; Zeelenberg, Cees; van Nimwegen, Chris

2001-01-01

Background The MEDICOM (Medical Products Electronic Commerce) Portal provides the electronic means for medical-equipment manufacturers to communicate online with their customers while supporting the Purchasing Process and Post Market Surveillance. The Portal offers a powerful Internet-based search tool for finding medical products and manufacturers. Its main advantage is the fast, reliable and up-to-date retrieval of information while eliminating all unrelated content that a general-purpose search engine would retrieve. The Universal Medical Device Nomenclature System (UMDNS) registers all products. The Portal accepts end-user requests and generates a list of results containing text descriptions of devices, UMDNS attribute values, and links to manufacturer Web pages and online catalogues for access to more-detailed information. Device short descriptions are provided by the corresponding manufacturer. The Portal offers technical support for integration of the manufacturers' Web sites with itself. The network of the Portal and the connected manufacturers' sites is called the MEDICOM system. Objective To establish an environment hosting all the interactions of consumers (health care organizations and professionals) and providers (manufacturers, distributors, and resellers of medical devices). Methods The Portal provides the end-user interface, implements system management, and supports database compatibility. The Portal hosts information about the whole MEDICOM system (Common Database) and summarized descriptions of medical devices (Short Description Database); the manufacturers' servers present extended descriptions. The Portal provides end-user profiling and registration, an efficient product-searching mechanism, bulletin boards, links to on-line libraries and standards, on-line information for the MEDICOM system, and special messages or advertisements from manufacturers. Platform independence and interoperability characterize the system design. Relational Database Management Systems are used for the system's databases. The end-user interface is implemented using HTML, Javascript, Java applets, and XML documents. Communication between the Portal and the manufacturers' servers is implemented using a CORBA interface. Remote administration of the Portal is enabled by dynamically-generated HTML interfaces based on XML documents. A representative group of users evaluated the system. The aim of the evaluation was validation of the usability of all of MEDICOM's functionality. The evaluation procedure was based on ISO/IEC 9126 Information technology - Software product evaluation - Quality characteristics and guidelines for their use. Results The overall user evaluation of the MEDICOM system was very positive. The MEDICOM system was characterized as an innovative concept that brings significant added value to medical-equipment commerce. Conclusions The eventual benefits of the MEDICOM system are (a) establishment of a worldwide-accessible marketplace between manufacturers and health care professionals that provides up-to-date and high-quality product information in an easy and friendly way and (b) enhancement of the efficiency of marketing procedures and after-sales support. PMID:11772547

XBRL: Beyond Basic XML

ERIC Educational Resources Information Center

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…

Querying and Ranking XML Documents.

ERIC Educational Resources Information Center

Schlieder, Torsten; Meuss, Holger

2002-01-01

Discussion of XML, information retrieval, precision, and recall focuses on a retrieval technique that adopts the similarity measure of the vector space model, incorporates the document structure, and supports structured queries. Topics include a query model based on tree matching; structured queries and term-based ranking; and term frequency and…

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2011-01-01

Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML). PMID:21464833

New NED XML/VOtable Services and Client Interface Applications

NASA Astrophysics Data System (ADS)

Pevunova, O.; Good, J.; Mazzarella, J.; Berriman, G. B.; Madore, B.

2005-12-01

The NASA/IPAC Extragalactic Database (NED) provides data and cross-identifications for over 7 million extragalactic objects fused from thousands of survey catalogs and journal articles. The data cover all frequencies from radio through gamma rays and include positions, redshifts, photometry and spectral energy distributions (SEDs), sizes, and images. NED services have traditionally supplied data in HTML format for connections from Web browsers, and a custom ASCII data structure for connections by remote computer programs written in the C programming language. We describe new services that provide responses from NED queries in XML documents compliant with the international virtual observatory VOtable protocol. The XML/VOtable services support cone searches, all-sky searches based on object attributes (survey names, cross-IDs, redshifts, flux densities), and requests for detailed object data. Initial services have been inserted into the NVO registry, and others will follow soon. The first client application is a Style Sheet specification for rendering NED VOtable query results in Web browsers that support XML. The second prototype application is a Java applet that allows users to compare multiple SEDs. The new XML/VOtable output mode will also simplify the integration of data from NED into visualization and analysis packages, software agents, and other virtual observatory applications. We show an example SED from NED plotted using VOPlot. The NED website is: http://nedwww.ipac.caltech.edu.

Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML.

PubMed

Rubin, Daniel L; Hewett, Micheal; Oliver, Diane E; Klein, Teri E; Altman, Russ B

2002-01-01

Ontologies are useful for organizing large numbers of concepts having complex relationships, such as the breadth of genetic and clinical knowledge in pharmacogenomics. But because ontologies change and knowledge evolves, it is time consuming to maintain stable mappings to external data sources that are in relational format. We propose a method for interfacing ontology models with data acquisition from external relational data sources. This method uses a declarative interface between the ontology and the data source, and this interface is modeled in the ontology and implemented using XML schema. Data is imported from the relational source into the ontology using XML, and data integrity is checked by validating the XML submission with an XML schema. We have implemented this approach in PharmGKB (http://www.pharmgkb.org/), a pharmacogenetics knowledge base. Our goals were to (1) import genetic sequence data, collected in relational format, into the pharmacogenetics ontology, and (2) automate the process of updating the links between the ontology and data acquisition when the ontology changes. We tested our approach by linking PharmGKB with data acquisition from a relational model of genetic sequence information. The ontology subsequently evolved, and we were able to rapidly update our interface with the external data and continue acquiring the data. Similar approaches may be helpful for integrating other heterogeneous information sources in order make the diversity of pharmacogenetics data amenable to computational analysis.

The XBabelPhish MAGE-ML and XML translator.

PubMed

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.

106-17 Telemetry Standards Metadata Configuration Chapter 23

DTIC Science & Technology

2017-07-01

23-1 23.2 Metadata Description Language ...Chapter 23, July 2017 iii Acronyms HTML Hypertext Markup Language MDL Metadata Description Language PCM pulse code modulation TMATS Telemetry...Attributes Transfer Standard W3C World Wide Web Consortium XML eXtensible Markup Language XSD XML schema document Telemetry Network Standard

Bridging the Gap in Port Security; Network Centric Theory Applied to Public/Private Collaboration

DTIC Science & Technology

2007-03-01

commercial_enforcement/ ctpat /security_guideline/guideline_port.xml [Accessed January 2, 2007] 16 The four core elements of CSI include:36 • Identify high...www.cbp.gov/xp/cgov/import/commercial_enforcement/ ctpat /security_guideline/guideline_port.xml [Accessed January 2, 2007]. 17 Connecting them

Converting from XML to HDF-EOS

NASA Technical Reports Server (NTRS)

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.

A Leaner, Meaner Markup Language.

ERIC Educational Resources Information Center

Online & CD-ROM Review, 1997

1997-01-01

In 1996 a working group of the World Wide Web Consortium developed and released a simpler form of markup language, Extensible Markup Language (XML), combining the flexibility of standard Generalized Markup Language (SGML) and the Web suitability of HyperText Markup Language (HTML). Reviews SGML and discusses XML's suitability for journal…

DoD Business Mission Area Service-Oriented Architecture to Support Business Transformation

DTIC Science & Technology

2008-10-01

Notation ( BPMN ). The research also found strong support across vendors for the Business Process Execution Language standard, though there is also...emerging support for direct execution of BPMN through the use of the XML Process Definition Language, an XML serialization of BPMN . Many vendors also

DocML: A Digital Library of University Data.

ERIC Educational Resources Information Center

Papadakis, Ioannis; Karakoidas, Vassileios; Chrissikopoulos, Vassileios

2002-01-01

Describes DocML, a Web-based digital library of university data that is used to build a system capable of preserving and managing student assignments. Topics include requirements for a digital library of university data; metadata and XML; three-tier architecture; user interface; searching; browsing; content delivery; and administrative issues.…

The JCMT Observatory Control System

NASA Astrophysics Data System (ADS)

Rees, Nick; Economou, Frossie; Jenness, Tim; Kackley, Russell; Walther, Craig; Dent, Bill; Folger, Martin; Gao, Xiaofeng; Kelly, Dennis; Lightfoot, John; Pain, Ian; Hovey, Gary; Willis, Tony; Redman, Russell

The JCMT, the world's largest sub-mm telescope, has had essentially the same VAX/VMS based control system since it was commissioned. For the next generation of instrumentation we are implementing a new Unix/VxWorks based system, based on the successful ORAC system that was recently released on UKIRT. This paper gives a broad overview of the system architecture and includes some discussion on the choices made. The pros and cons of using XML as an inherent part of the system architecture are also discussed.

THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA

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

Devarakonda, Ranjeet; Shrestha, Biva; Palanisamy, Giri

Nobody is better suited to describe data than the scientist who created it. This description about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset [1]. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, andmore » locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [2][4]. OME is part of ORNL s Mercury software fleet [2][3]. It was jointly developed to support projects funded by the United States Geological Survey (USGS), U.S. Department of Energy (DOE), National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA). OME s architecture provides a customizable interface to support project-specific requirements. Using this new architecture, the ORNL team developed OME instances for USGS s Core Science Analytics, Synthesis, and Libraries (CSAS&L), DOE s Next Generation Ecosystem Experiments (NGEE) and Atmospheric Radiation Measurement (ARM) Program, and the international Surface Ocean Carbon Dioxide ATlas (SOCAT). Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. From the information on the form, the Metadata Editor can create an XML file on the server that the editor is installed or to the user s personal computer. Researchers can also use the ORNL Metadata Editor to modify existing XML metadata files. As an example, an NGEE Arctic scientist use OME to register their datasets to the NGEE data archive and allows the NGEE archive to publish these datasets via a data search portal (http://ngee.ornl.gov/data). These highly descriptive metadata created using OME allows the Archive to enable advanced data search options using keyword, geo-spatial, temporal and ontology filters. Similarly, ARM OME allows scientists or principal investigators (PIs) to submit their data products to the ARM data archive. How would OME help Big Data Centers like the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC)? The ORNL DAAC is one of NASA s Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data. OME will allow data centers like the NGEE and ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability. Useful Links: USGS OME: http://mercury.ornl.gov/OME/ NGEE OME: http://ngee-arctic.ornl.gov/ngeemetadata/ ARM OME: http://archive2.ornl.gov/armome/ Contact: Ranjeet Devarakonda (devarakondar@ornl.gov) References: [1] Federal Geographic Data Committee. Content standard for digital geospatial metadata. Federal Geographic Data Committee, 1998. [2] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94. [3] Wilson, B. E., Palanisamy, G., Devarakonda, R., Rhyne, B. T., Lindsley, C., & Green, J. (2010). Mercury Toolset for Spatiotemporal Metadata. [4] Pouchard, L. C., Branstetter, M. L., Cook, R. B., Devarakonda, R., Green, J., Palanisamy, G., ... & Noy, N. F. (2013). A Linked Science investigation: enhancing climate change data discovery with semantic technologies. Earth science informatics, 6(3), 175-185.« less

Reference Architecture for MNE 5 Technical System

DTIC Science & Technology

2007-05-30

of being available in most experiments. Core Services A core set of applications whi directories, web portal and collaboration applications etc. A...classifications Messages (xml, JMS, content level…) Meta data filtering, who can initiate services Web browsing Collaboration & messaging Border...Exchange Ref Architecture for MNE5 Tech System.doc 9 of 21 audit logging Person and machine Data lev objects, web services, messages rification el

Experiences Obtained with Integration of Student Response Systems for iPod Touch and iPhone into e-Learning Environments

ERIC Educational Resources Information Center

Stav, John; Nielsen, Kjetil; Hansen-Nygard, Gabrielle; Thorseth, Trond

2010-01-01

A new type of Student Response System (SRS) based up on the latest wireless technologies and hand held mobile devices has been developed to enhance active learning methods and assess students' understanding. The key services involve a set of XML technologies, web services and modern mobile devices. A group consisting of engineers, scientists and…

Beyond the New Architectures - Enabling Rapid System Configurations

NASA Technical Reports Server (NTRS)

Smith, Dan

2009-01-01

This presentation slide document reviews the attempts to integrate systems and create common standards for missions. A primary example is telemetry and command sets for satellites. The XML Telemetric and Command Exchange (XTCE) exists, but this is not easy to implement. There is a need for a new standard. The document proposes a method to achieve the standard, and the benefits of using a new standard,

An Approach to Dynamic Service Management in Pervasive Computing Systems

DTIC Science & Technology

2005-01-01

standard interface to them that is easily accessible by any user. This paper outlines the design of Centaurus , an infrastructure for presenting...based on Extensi- ble Markup Language (XML) for communication, giving the system a uniform and easily adaptable interface. Centaurus defines a...easy and automatic usage. This is the vision that guides our re- search on the Centaurus system. We define a SmartSpace as a dynamic environment that

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

NASA Astrophysics Data System (ADS)

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

2005-11-01

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

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

2015-10-01

In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

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

USGS Publications Warehouse

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

2005-01-01

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

The application of geography markup language (GML) to the geological sciences

NASA Astrophysics Data System (ADS)

Lake, Ron

2005-11-01

GML 3.0 became an adopted specification of the Open Geospatial Consortium (OGC) in January 2003, and is rapidly emerging as the world standard for the encoding, transport and storage of all forms of geographic information. This paper looks at the application of GML to one of the more challenging areas of automated geography, namely the geological sciences. Specific features of GML of interest to geologists are discussed and then illustrated through a series of geological case studies. We conclude the paper with a discussion of anticipated geological web services that GML will enable. GML is written in XML and makes use of XML Schema for extensibility. It can be used both to represent or model geographic objects and to transport them across the Internet. In this way it serves as the foundation for all manner of geographic web services. Unlike vertical application grammars such as LandXML, GML was intended to define geographic application languages, and hence is applicable to any geographic domain including forestry, environmental sciences, geology and oceanography. This paper provides a review of the basic features of GML that are fundamental to the geological sciences including geometry, coverages, observations, reference systems and temporality. These constructs are then employed in a series of simple geological case studies including structural geological description, surficial geology, representation of geological time scales, mineral occurrences, geohazards and geochemical reconnaissance.

Integration of HTML documents into an XML-based knowledge repository.

PubMed

Roemer, Lorrie K; Rocha, Roberto A; Del Fiol, Guilherme

2005-01-01

The Emergency Patient Instruction Generator (EPIG) is an electronic content compiler / viewer / editor developed by Intermountain Health Care. The content is vendor-licensed HTML patient discharge instructions. This work describes the process by which discharge instructions where converted from ASCII-encoded HTML to XML, then loaded to a database for use by EPIG.

A Survey and Analysis of Access Control Architectures for XML Data

DTIC Science & Technology

2006-03-01

13 4. XML Query Engines ...castle and the drawbridge over the moat. Extending beyond the visual analogy, there are many key components to the protection of information and...technology. While XML’s original intent was to enable large-scale electronic publishing over the internet, its functionality is firmly rooted in its

Personalization of XML Content Browsing Based on User Preferences

ERIC Educational Resources Information Center

Encelle, Benoit; Baptiste-Jessel, Nadine; Sedes, Florence

2009-01-01

Personalization of user interfaces for browsing content is a key concept to ensure content accessibility. In this direction, we introduce concepts that result in the generation of personalized multimodal user interfaces for browsing XML content. User requirements concerning the browsing of a specific content type can be specified by means of…

A Conversion Tool for Mathematical Expressions in Web XML Files.

ERIC Educational Resources Information Center

Ohtake, Nobuyuki; Kanahori, Toshihiro

2003-01-01

This article discusses the conversion of mathematical equations into Extensible Markup Language (XML) on the World Wide Web for individuals with visual impairments. A program is described that converts the presentation markup style to the content markup style in MathML to allow browsers to render mathematical expressions without other programs.…

Strategic Industrial Alliances in Paper Industry: XML- vs Ontology-Based Integration Platforms

ERIC Educational Resources Information Center

Naumenko, Anton; Nikitin, Sergiy; Terziyan, Vagan; Zharko, Andriy

2005-01-01

Purpose: To identify cases related to design of ICT platforms for industrial alliances, where the use of Ontology-driven architectures based on Semantic web standards is more advantageous than application of conventional modeling together with XML standards. Design/methodology/approach: A comparative analysis of the two latest and the most obvious…

Experimental Evaluation of Processing Time for the Synchronization of XML-Based Business Objects

NASA Astrophysics Data System (ADS)

Ameling, Michael; Wolf, Bernhard; Springer, Thomas; Schill, Alexander

Business objects (BOs) are data containers for complex data structures used in business applications such as Supply Chain Management and Customer Relationship Management. Due to the replication of application logic, multiple copies of BOs are created which have to be synchronized and updated. This is a complex and time consuming task because BOs rigorously vary in their structure according to the distribution, number and size of elements. Since BOs are internally represented as XML documents, the parsing of XML is one major cost factor which has to be considered for minimizing the processing time during synchronization. The prediction of the parsing time for BOs is an significant property for the selection of an efficient synchronization mechanism. In this paper, we present a method to evaluate the influence of the structure of BOs on their parsing time. The results of our experimental evaluation incorporating four different XML parsers examine the dependencies between the distribution of elements and the parsing time. Finally, a general cost model will be validated and simplified according to the results of the experimental setup.

Rock.XML - Towards a library of rock physics models

NASA Astrophysics Data System (ADS)

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.

TU-CD-304-11: Veritas 2.0: A Cloud-Based Tool to Facilitate Research and Innovation

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

Mishra, P; Patankar, A; Etmektzoglou, A

Purpose: We introduce Veritas 2.0, a cloud-based, non-clinical research portal, to facilitate translation of radiotherapy research ideas to new delivery techniques. The ecosystem of research tools includes web apps for a research beam builder for TrueBeam Developer Mode, an image reader for compressed and uncompressed XIM files, and a trajectory log file based QA/beam delivery analyzer. Methods: The research beam builder can generate TrueBeam readable XML file either from scratch or from pre-existing DICOM-RT plans. DICOM-RT plan is first converted to XML format and then researcher can interactively modify or add control points to them. Delivered beam can be verifiedmore » via reading generated images and analyzing trajectory log files. Image reader can read both uncompressed and HND-compressed XIM images. The trajectory log analyzer lets researchers plot expected vs. actual values and deviations among 30 mechanical axes. The analyzer gives an animated view of MLC patterns for the beam delivery. Veritas 2.0 is freely available and its advantages versus standalone software are i) No software installation or maintenance needed, ii) easy accessibility across all devices iii) seamless upgrades and iv) OS independence. Veritas is written using open-source tools like twitter bootstrap, jQuery, flask, and Python-based modules. Results: In the first experiment, an anonymized 7-beam DICOM-RT IMRT plan was converted to XML beam containing 1400 control points. kV and MV imaging points were inserted into this XML beam. In another experiment, a binary log file was analyzed to compare actual vs expected values and deviations among axes. Conclusions: Veritas 2.0 is a public cloud-based web app that hosts a pool of research tools for facilitating research from conceptualization to verification. It is aimed at providing a platform for facilitating research and collaboration. I am full time employee at Varian Medical systems, Palo Alto.« less

Progress on an implementation of MIFlowCyt in XML

NASA Astrophysics Data System (ADS)

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.

Application of XML to Journal Table Archiving

NASA Astrophysics Data System (ADS)

Shaya, E. J.; Blackwell, J. H.; Gass, J. E.; Kargatis, V. E.; Schneider, G. L.; Weiland, J. L.; Borne, K. D.; White, R. A.; Cheung, C. Y.

1998-12-01

The Astronomical Data Center (ADC) at the NASA Goddard Space Flight Center is a major archive for machine-readable astronomical data tables. Many ADC tables are derived from published journal articles. Article tables are reformatted to be machine-readable and documentation is crafted to facilitate proper reuse by researchers. The recent switch of journals to web based electronic format has resulted in the generation of large amounts of tabular data that could be captured into machine-readable archive format at fairly low cost. The large data flow of the tables from all major North American astronomical journals (a factor of 100 greater than the present rate at the ADC) necessitates the development of rigorous standards for the exchange of data between researchers, publishers, and the archives. We have selected a suitable markup language that can fully describe the large variety of astronomical information contained in ADC tables. The eXtensible Markup Language XML is a powerful internet-ready documentation format for data. It provides a precise and clear data description language that is both machine- and human-readable. It is rapidly becoming the standard format for business and information transactions on the internet and it is an ideal common metadata exchange format. By labelling, or "marking up", all elements of the information content, documents are created that computers can easily parse. An XML archive can easily and automatically be maintained, ingested into standard databases or custom software, and even totally restructured whenever necessary. Structuring astronomical data into XML format will enable efficient and focused search capabilities via off-the-shelf software. The ADC is investigating XML's expanded hyperlinking power to enhance connectivity within the ADC data/metadata and developing XSL display scripts to enhance display of astronomical data. The ADC XML Definition Type Document can be viewed at http://messier.gsfc.nasa.gov/dtdhtml/DTD-TREE.html

The Service Environment for Enhanced Knowledge and Research (SEEKR) Framework

NASA Astrophysics Data System (ADS)

King, T. A.; Walker, R. J.; Weigel, R. S.; Narock, T. W.; McGuire, R. E.; Candey, R. M.

2011-12-01

The Service Environment for Enhanced Knowledge and Research (SEEKR) Framework is a configurable service oriented framework to enable the discovery, access and analysis of data shared in a community. The SEEKR framework integrates many existing independent services through the use of web technologies and standard metadata. Services are hosted on systems by using an application server and are callable by using REpresentational State Transfer (REST) protocols. Messages and metadata are transferred with eXtensible Markup Language (XML) encoding which conform to a published XML schema. Space Physics Archive Search and Extract (SPASE) metadata is central to utilizing the services. Resources (data, documents, software, etc.) are described with SPASE and the associated Resource Identifier is used to access and exchange resources. The configurable options for the service can be set by using a web interface. Services are packaged as web application resource (WAR) files for direct deployment on application services such as Tomcat or Jetty. We discuss the composition of the SEEKR framework, how new services can be integrated and the steps necessary to deploying the framework. The SEEKR Framework emerged from NASA's Virtual Magnetospheric Observatory (VMO) and other systems and we present an overview of these systems from a SEEKR Framework perspective.

Force-directed visualization for conceptual data models

NASA Astrophysics Data System (ADS)

Battigaglia, Andrew; Sutter, Noah

2017-03-01

Conceptual data models are increasingly stored in an eXtensible Markup Language (XML) format because of its portability between different systems and the ability of databases to use this format for storing data. However, when attempting to capture business or design needs, an organized graphical format is preferred in order to facilitate communication to receive as much input as possible from users and subject-matter experts. Existing methods of achieving this conversion suffer from problems of not being specific enough to capture all of the needs of conceptual data modeling and not being able to handle a large number of relationships between entities. This paper describes an implementation for a modeling solution to clearly illustrate conceptual data models stored in XML formats in well organized and structured diagrams. A force layout with several different parameters is applied to the diagram to create both compact and easily traversable relationships between entities.

Future perspectives - proposal for Oxford Physiome Project.

PubMed

Oku, Yoshitaka

2010-01-01

The Physiome Project is an effort to understand living creatures using "analysis by synthesis" strategy, i.e., by reproducing their behaviors. In order to achieve its goal, sharing developed models between different computer languages and application programs to incorporate into integrated models is critical. To date, several XML-based markup languages has been developed for this purpose. However, source codes written with XML-based languages are very difficult to read and edit using text editors. An alternative way is to use an object-oriented meta-language, which can be translated to different computer languages and transplanted to different application programs. Object-oriented languages are suitable for describing structural organization by hierarchical classes and taking advantage of statistical properties to reduce the number of parameter while keeping the complexity of behaviors. Using object-oriented languages to describe each element and posting it to a public domain should be the next step to build up integrated models of the respiratory control system.

Development of the Plate Tectonics and Seismology markup languages with XML

NASA Astrophysics Data System (ADS)

Babaie, H.; Babaei, A.

2003-04-01

The Extensible Markup Language (XML) and its specifications such as the XSD Schema, allow geologists to design discipline-specific vocabularies such as Seismology Markup Language (SeismML) or Plate Tectonics Markup Language (TectML). These languages make it possible to store and interchange structured geological information over the Web. Development of a geological markup language requires mapping geological concepts, such as "Earthquake" or "Plate" into a UML object model, applying a modeling and design environment. We have selected four inter-related geological concepts: earthquake, fault, plate, and orogeny, and developed four XML Schema Definitions (XSD), that define the relationships, cardinalities, hierarchies, and semantics of these concepts. In such a geological concept model, the UML object "Earthquake" is related to one or more "Wave" objects, each arriving to a seismic station at a specific "DateTime", and relating to a specific "Epicenter" object that lies at a unique "Location". The "Earthquake" object occurs along a "Segment" of a "Fault" object, which is related to a specific "Plate" object. The "Fault" has its own associations with such things as "Bend", "Step", and "Segment", and could be of any kind (e.g., "Thrust", "Transform'). The "Plate" is related to many other objects such as "MOR", "Subduction", and "Forearc", and is associated with an "Orogeny" object that relates to "Deformation" and "Strain" and several other objects. These UML objects were mapped into XML Metadata Interchange (XMI) formats, which were then converted into four XSD Schemas. The schemas were used to create and validate the XML instance documents, and to create a relational database hosting the plate tectonics and seismological data in the Microsoft Access format. The SeismML and TectML allow seismologists and structural geologists, among others, to submit and retrieve structured geological data on the Internet. A seismologist, for example, can submit peer-reviewed and reliable data about a specific earthquake to a Java Server Page on our web site hosting the XML application. Other geologists can readily retrieve the submitted data, saved in files or special tables of the designed database, through a search engine designed with J2EE (JSP, servlet, Java Bean) and XML specifications such as XPath, XPointer, and XSLT. When extended to include all the important concepts of seismology and plate tectonics, the two markup languages will make global interchange of geological data a reality.

Factors to keep in mind when introducing virtual microscopy.

PubMed

Glatz-Krieger, Katharina; Spornitz, Udo; Spatz, Alain; Mihatsch, Michael J; Glatz, Dieter

2006-03-01

Digitization of glass slides and delivery of so-called virtual slides (VS) emulating a real microscope over the Internet have become reality due to recent improvements in technology. We have implemented a virtual microscope for instruction of medical students and for continuing medical education. Up to 30,000 images per slide are captured using a microscope with an automated stage. The images are post-processed and then served by a plain hypertext transfer protocol (http)-server. A virtual slide client (vMic) based on Macromedia's Flash MX, a highly accepted technology available on every modern Web browser, has been developed. All necessary virtual slide parameters are stored in an XML file together with the image. Evaluation of the courses by questionnaire indicated that most students and many but not all pathologists regard virtual slides as an adequate replacement for traditional slides. All our virtual slides are publicly accessible over the World Wide Web (WWW) at http://vmic.unibas.ch . Recently, several commercially available virtual slide acquisition systems (VSAS) have been developed that use various technologies to acquire and distribute virtual slides. These systems differ in speed, image quality, compatibility, viewer functionalities and price. This paper gives an overview of the factors to keep in mind when introducing virtual microscopy.

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

CCSDS Overview

NASA Technical Reports Server (NTRS)

Kearney, Mike

2013-01-01

The primary goal of Consultative Committee for Space Data Systems (CCSDS) is interoperability between communications and data systems of space agencies' vehicles, facilities, missions and programs. Of all of the technologies used in spaceflight, standardization of communications and data systems brings the most benefit to multi-agency interoperability. CCSDS Started in 1982 developing standards at the lower layers of the protocol stack. The CCSDS scope has grown to cover standards throughout the entire ISO communications stack, plus other Data Systems areas (architecture, archive, security, XML exchange formats, etc.

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

Our purpose was to build and test a lightweight solution for generating clinical research information systems (CRIS) that would allow non-IT professionals with basic knowledge of computer usage to quickly define and build a ready-to-use, safe and secure web-based clinical research system for data management. We use the acronym MAGIC (Medical Application Generator InteraCtive) for the system. The generated CRIS should be very easy to build and use, so a common LAMP (Linux Apache MySQL Perl) platform was used, which also enables short development cycles. The application was built and tested using eXtreme Programming (XP) principles by a small development team consisting of one informatics specialist, one physician and one graphical designer/programmer. The parameter and graphical user interface (GUI) definitions for the CRIS can be made by non-IT professionals using an intuitive English-language-like formalism called application definition language (ADL). From these definitions, the MAGIC builds an end-user CRIS that can be used on a wide variety of platforms (from standard workstations to hand-held devices). A working example of a national health-care-quality assessment program is presented to illustrate this process. The lightweight application for generating CRIS (MAGIC) has proven to be useful for both clinical and analytical users in real working environment. To achieve better performance and interoperability, we are planning to recompile the application using XML schemas (XSD) in HL7 CDA or openEHR archetypes formats used for parameters definition and for data interchange between different information systems.

76 FR 4897 - Submission for OMB Review; OMB Control No. 3090-0291; FSRS Registration and Prime Awardee Entity...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

... methods for submitting multiple FFATA subaward reports: A batch upload template using Microsoft Excel, an... three methods for submitting multiple FFATA subaward reports: A batch upload template using Microsoft Excel, an XML report submission template and an XML web service. These methods do take advantage of the...

Integration of HTML Documents into an XML-Based Knowledge Repository

PubMed Central

Roemer, Lorrie K; Rocha, Roberto A; Del Fiol, Guilherme

2005-01-01

The Emergency Patient Instruction Generator (EPIG) is an electronic content compiler/viewer/editor developed by Intermountain Health Care. The content is vendor-licensed HTML patient discharge instructions. This work describes the process by which discharge instructions where converted from ASCII-encoded HTML to XML, then loaded to a database for use by EPIG. PMID:16779384

International Data | Geospatial Data Science | NREL

Science.gov Websites

International Data International Data These datasets detail solar and wind resources for select Annual.xml India 10-km Monthly Direct Normal and Global Horizontal Zip 4.68 MB 04/25/2013 Monthly.xml Wind Data 50-m Wind Data These 50-m hub-height datasets have been validated by NREL and wind energy

Compression-based aggregation model for medical web services.

PubMed

Al-Shammary, Dhiah; Khalil, Ibrahim

2010-01-01

Many organizations such as hospitals have adopted Cloud Web services in applying their network services to avoid investing heavily computing infrastructure. SOAP (Simple Object Access Protocol) is the basic communication protocol of Cloud Web services that is XML based protocol. Generally,Web services often suffer congestions and bottlenecks as a result of the high network traffic that is caused by the large XML overhead size. At the same time, the massive load on Cloud Web services in terms of the large demand of client requests has resulted in the same problem. In this paper, two XML-aware aggregation techniques that are based on exploiting the compression concepts are proposed in order to aggregate the medical Web messages and achieve higher message size reduction.

Representation of thermal infrared imaging data in the DICOM using XML configuration files.

PubMed

Ruminski, Jacek

2007-01-01

The DICOM standard has become a widely accepted and implemented format for the exchange and storage of medical imaging data. Different imaging modalities are supported however there is not a dedicated solution for thermal infrared imaging in medicine. In this article we propose new ideas and improvements to final proposal of the new DICOM Thermal Infrared Imaging structures and services. Additionally, we designed, implemented and tested software packages for universal conversion of existing thermal imaging files to the DICOM format using XML configuration files. The proposed solution works fast and requires minimal number of user interactions. The XML configuration file enables to compose a set of attributes for any source file format of thermal imaging camera.

Bioinformatics data distribution and integration via Web Services and XML.

PubMed

Li, Xiao; Zhang, Yizheng

2003-11-01

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

QuakeML - An XML Schema for Seismology

NASA Astrophysics Data System (ADS)

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.

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

XM1 Gunnery Training and Aptitude Requirements Analyses

DTIC Science & Technology

1981-02-01

of the XML tank weapons system. Army materiel systems such as the XK tank are initiated, developed, de - ployed, supported, modified and disposed in...Analysis ( TASA ) to satisfy the FEA requirement. Users of the TASA at the Armor School were uniformly critical of the work. Generally described as...inaccurate, incomplete and to a large extent, obsolete the TASA failed to provide the information necessary for addressing the concerns of future operators

SBRML: a markup language for associating systems biology data with models.

PubMed

Dada, Joseph O; Spasić, Irena; Paton, Norman W; Mendes, Pedro

2010-04-01

Research in systems biology is carried out through a combination of experiments and models. Several data standards have been adopted for representing models (Systems Biology Markup Language) and various types of relevant experimental data (such as FuGE and those of the Proteomics Standards Initiative). However, until now, there has been no standard way to associate a model and its entities to the corresponding datasets, or vice versa. Such a standard would provide a means to represent computational simulation results as well as to frame experimental data in the context of a particular model. Target applications include model-driven data analysis, parameter estimation, and sharing and archiving model simulations. We propose the Systems Biology Results Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each dataset is represented as a series of values associated with model variables, and their corresponding parameter values. SBRML provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes. We present and discuss several examples of SBRML usage in applications such as enzyme kinetics, microarray gene expression and various types of simulation results. The XML Schema file for SBRML is available at http://www.comp-sys-bio.org/SBRML under the Academic Free License (AFL) v3.0.

X-PAT: a multiplatform patient referral data management system for small healthcare institution requirements.

PubMed

Masseroli, Marco; Marchente, Mario

2008-07-01

We present X-PAT, a platform-independent software prototype that is able to manage patient referral multimedia data in an intranet network scenario according to the specific control procedures of a healthcare institution. It is a self-developed storage framework based on a file system, implemented in eXtensible Markup Language (XML) and PHP Hypertext Preprocessor Language, and addressed to the requirements of limited-dimension healthcare entities (small hospitals, private medical centers, outpatient clinics, and laboratories). In X-PAT, healthcare data descriptions, stored in a novel Referral Base Management System (RBMS) according to Health Level 7 Clinical Document Architecture Release 2 (CDA R2) standard, can be easily applied to the specific data and organizational procedures of a particular healthcare working environment thanks also to the use of standard clinical terminology. Managed data, centralized on a server, are structured in the RBMS schema using a flexible patient record and CDA healthcare referral document structures based on XML technology. A novel search engine allows defining and performing queries on stored data, whose rapid execution is ensured by expandable RBMS indexing structures. Healthcare personnel can interface the X-PAT system, according to applied state-of-the-art privacy and security measures, through friendly and intuitive Web pages that facilitate user acceptance.

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface.

PubMed

Briache, Abdelaali; Marrakchi, Kamar; Kerzazi, Amine; Navas-Delgado, Ismael; Rossi Hassani, Badr D; Lairini, Khalid; Aldana-Montes, José F

2012-01-25

Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data. To provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface. YeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/.

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

NASA Astrophysics Data System (ADS)

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 convert both historic and modern-day MT or related transfer functions into the searchable database at the IRIS DMC. The more complete and free access to these previously collected MT TFs will be of great value to MT scientists both in planning future surveys, and then to leverage the value of the new data at the inversion and interpretation stage.

Creating preservation metadata from XML-metadata profiles

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Bertelmann, Roland; Gebauer, Petra; Hasler, Tim; Klump, Jens; Kirchner, Ingo; Peters-Kottig, Wolfgang; Mettig, Nora; Rusch, Beate

2014-05-01

Registration of dataset DOIs at DataCite makes research data citable and comes with the obligation to keep data accessible in the future. In addition, many universities and research institutions measure data that is unique and not repeatable like the data produced by an observational network and they want to keep these data for future generations. In consequence, such data should be ingested in preservation systems, that automatically care for file format changes. Open source preservation software that is developed along the definitions of the ISO OAIS reference model is available but during ingest of data and metadata there are still problems to be solved. File format validation is difficult, because format validators are not only remarkably slow - due to variety in file formats different validators return conflicting identification profiles for identical data. These conflicts are hard to resolve. Preservation systems have a deficit in the support of custom metadata. Furthermore, data producers are sometimes not aware that quality metadata is a key issue for the re-use of data. In the project EWIG an university institute and a research institute work together with Zuse-Institute Berlin, that is acting as an infrastructure facility, to generate exemplary workflows for research data into OAIS compliant archives with emphasis on the geosciences. The Institute for Meteorology provides timeseries data from an urban monitoring network whereas GFZ Potsdam delivers file based data from research projects. To identify problems in existing preservation workflows the technical work is complemented by interviews with data practitioners. Policies for handling data and metadata are developed. Furthermore, university teaching material is created to raise the future scientists awareness of research data management. As a testbed for ingest workflows the digital preservation system Archivematica [1] is used. During the ingest process metadata is generated that is compliant to the Metadata Encoding and Transmission Standard (METS). To find datasets in future portals and to make use of this data in own scientific work, proper selection of discovery metadata and application metadata is very important. Some XML-metadata profiles are not suitable for preservation, because version changes are very fast and make it nearly impossible to automate the migration. For other XML-metadata profiles schema definitions are changed after publication of the profile or the schema definitions become inaccessible, which might cause problems during validation of the metadata inside the preservation system [2]. Some metadata profiles are not used widely enough and might not even exist in the future. Eventually, discovery and application metadata have to be embedded into the mdWrap-subtree of the METS-XML. [1] http://www.archivematica.org [2] http://dx.doi.org/10.2218/ijdc.v7i1.215

TileDCS web system

NASA Astrophysics Data System (ADS)

Maidantchik, C.; Ferreira, F.; Grael, F.; Atlas Tile Calorimeter Community

2010-04-01

The web system described here provides features to monitor the ATLAS Detector Control System (DCS) acquired data. The DCS is responsible for overseeing the coherent and safe operation of the ATLAS experiment hardware. In the context of the Hadronic Tile Calorimeter Detector (TileCal), it controls the power supplies of the readout electronics acquiring voltages, currents, temperatures and coolant pressure measurements. The physics data taking requires the stable operation of the power sources. The TileDCS Web System retrieves automatically data and extracts the statistics for given periods of time. The mean and standard deviation outcomes are stored as XML files and are compared to preset thresholds. Further, a graphical representation of the TileCal cylinders indicates the state of the supply system of each detector drawer. Colors are designated for each kind of state. In this way problems are easier to find and the collaboration members can focus on them. The user selects a module and the system presents detailed information. It is possible to verify the statistics and generate charts of the parameters over the time. The TileDCS Web System also presents information about the power supplies latest status. One wedge is colored green whenever the system is on. Otherwise it is colored red. Furthermore, it is possible to perform customized analysis. It provides search interfaces where the user can set the module, parameters, and the time period of interest. The system also produces the output of the retrieved data as charts, XML files, CSV and ROOT files according to the user's choice.

Proper Plugin Protocols

DTIC Science & Technology

2011-12-28

specify collaboration constraints that occur in Java and XML frameworks and that the collaboration constraints from these frameworks matter in practice. (a...programming language boundaries, and Chapter 6 and Appendix A demonstrate that Fusion can specify constraints across both Java and XML in practice. (c...designed JUnit, Josh Bloch designed Java Collec- tions, and Krzysztof Cwalina designed the .NET Framework APIs. While all of these frameworks are very

Tomcat, Oracle & XML Web Archive

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

Cothren, D. C.

2008-01-01

The TOX (Tomcat Oracle & XML) web archive is a foundation for development of HTTP-based applications using Tomcat (or some other servlet container) and an Oracle RDBMS. Use of TOX requires coding primarily in PL/SQL, JavaScript, and XSLT, but also in HTML, CSS and potentially Java. Coded in Java and PL/SQL itself, TOX provides the foundation for more complex applications to be built.

77 FR 28541 - Request for Comments on the Recommendation for the Disclosure of Sequence Listings Using XML...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-15

... (EPO) as the lead, to propose a revised standard for the filing of nucleotide and/or amino acid.... ST.25 uses a controlled vocabulary of feature keys to describe nucleic acid and amino acid sequences... patent data purposes. The XML standard also includes four qualifiers for amino acids. These feature keys...

Integrating XQuery-Enabled SCORM XML Metadata Repositories into an RDF-Based E-Learning P2P Network

ERIC Educational Resources Information Center

Qu, Changtao; Nejdl, Wolfgang

2004-01-01

Edutella is an RDF-based E-Learning P2P network that is aimed to accommodate heterogeneous learning resource metadata repositories in a P2P manner and further facilitate the exchange of metadata between these repositories based on RDF. Whereas Edutella provides RDF metadata repositories with a quite natural integration approach, XML metadata…

Using Extensible Markup Language (XML) for the Single Source Delivery of Educational Resources by Print and Online: A Case Study

ERIC Educational Resources Information Center

Walsh, Lucas

2007-01-01

This article seeks to provide an introduction to Extensible Markup Language (XML) by looking at its use in a single source publishing approach to the provision of teaching resources in both hardcopy and online. Using the development of the International Baccalaureate Organisation's online Economics Subject Guide as a practical example, this…

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

PubMed

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

2001-01-01

The purpose of guidelines in clinical practice is to improve the effectiveness and efficiency of clinical care. It is known that nationally or internationally produced guidelines which, in particular, do not involve medical processes at the time of consultation, do not take local factors into account, and have no consistent implementation strategy, have limited impact in changing either the behaviour of physicians, or patterns of care. The literature provides evidence for the effectiveness of computerization of CPGs for increasing compliance and improving patient outcomes. Probably the most effective concepts are knowledge-based functions for decision support or monitoring that are integrated in clinical information systems. This approach is mostly restricted by the effort required for development and maintenance of the information systems and the limited number of implemented medical rules. Most of the guidelines are text-based, and are primarily published in medical journals and posted on the internet. However, internet-published guidelines have little impact on the behaviour of physicians. It can be difficult and time-consuming to browse the internet to find (a) the correct guidelines to an existing diagnosis and (b) and adequate recommendation for a specific clinical problem. Our objective is to provide a web-based guideline service that takes as input clinical data on a particular patient and returns as output a customizable set of recommendations regarding diagnosis and treatment. Information in healthcare is to a very large extent transmitted and stored as unstructured or slightly structured text such as discharge letters, reports, forms, etc. The same applies for facilities containing medical information resources for clinical purposes and research such as text books, articles, guidelines, etc. Physicians are used to obtaining information from text-based sources. Since most guidelines are text-based, it would be practical to use a document-based solution 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.

Multi-Criteria Adaptation in a Personalized Multimedia Testing Tool Based on Semantic Technologies

ERIC Educational Resources Information Center

Lazarinis, Fotis; Green, Steve; Pearson, Elaine

2011-01-01

In this article, we present the characteristics and the design of a modular personalized multimedia testing tool based fully on XML learning specifications. Personalization is based on the characteristics of the individual learners, thus the testing paths are tailored to their needs and goals. The system maintains learner profiles rich in content…

Light at Night Markup Language (LANML): XML Technology for Light at Night Monitoring Data

NASA Astrophysics Data System (ADS)

Craine, B. L.; Craine, E. R.; Craine, E. M.; Crawford, D. L.

2013-05-01

Light at Night Markup Language (LANML) is a standard, based upon XML, useful in acquiring, validating, transporting, archiving and analyzing multi-dimensional light at night (LAN) datasets of any size. The LANML standard can accommodate a variety of measurement scenarios including single spot measures, static time-series, web based monitoring networks, mobile measurements, and airborne measurements. LANML is human-readable, machine-readable, and does not require a dedicated parser. In addition LANML is flexible; ensuring future extensions of the format will remain backward compatible with analysis software. The XML technology is at the heart of communicating over the internet and can be equally useful at the desktop level, making this standard particularly attractive for web based applications, educational outreach and efficient collaboration between research groups.

Event Recording Data Acquisition System and Experiment Data Management System for Neutron Experiments at MLF, J-PARC

NASA Astrophysics Data System (ADS)

Nakatani, T.; Inamura, Y.; Moriyama, K.; Ito, T.; Muto, S.; Otomo, T.

Neutron scattering can be a powerful probe in the investigation of many phenomena in the materials and life sciences. The Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex (J-PARC) is a leading center of experimental neutron science and boasts one of the most intense pulsed neutron sources in the world. The MLF currently has 18 experimental instruments in operation that support a wide variety of users from across a range of research fields. The instruments include optical elements, sample environment apparatus and detector systems that are controlled and monitored electronically throughout an experiment. Signals from these components and those from the neutron source are converted into a digital format by the data acquisition (DAQ) electronics and recorded as time-tagged event data in the DAQ computers using "DAQ-Middleware". Operating in event mode, the DAQ system produces extremely large data files (˜GB) under various measurement conditions. Simultaneously, the measurement meta-data indicating each measurement condition is recorded in XML format by the MLF control software framework "IROHA". These measurement event data and meta-data are collected in the MLF common storage and cataloged by the MLF Experimental Database (MLF EXP-DB) based on a commercial XML database. The system provides a web interface for users to manage and remotely analyze experimental data.

A Real-Time System for Abusive Network Traffic Detection

DTIC Science & Technology

2011-03-01

examine the spamming behavior at the network layer (IP layer) by correlating data collected from three sources: a sinkhole , a large e-mail provider, and...which spam originates • autonomous systems that sent spam messages to their sinkhole • BGP route announcements With respect to IP address space, their...applications or machines to communicate with each other. They exchange XML- formatted data [58] using the HTTP [59] protocol. Specifically, the client uses the

C2 Core and UCore Message Design Capstone: Interoperable Message Structure

DTIC Science & Technology

2009-09-01

there are sufficient resources to carry out a mission. The Team used the Theatre Battle Management Command System ( TBMCS ) to generate sample CMD...System ( TBMCS ) was used to generate CMD messages as inputs for both use cases. These were programmatically transformed into the three-layer message...used for the experiment was generated from the TBMCS in the form of a CMD XML document. The Capstone experiment included transforming that document to

TiD-Introducing and Benchmarking an Event-Delivery System for Brain-Computer Interfaces.

PubMed

Breitwieser, Christian; Tavella, Michele; Schreuder, Martijn; Cincotti, Febo; Leeb, Robert; Muller-Putz, Gernot R

2017-12-01

In this paper, we present and analyze an event distribution system for brain-computer interfaces. Events are commonly used to mark and describe incidents during an experiment and are therefore critical for later data analysis or immediate real-time processing. The presented approach, called Tools for brain-computer interaction interface D (TiD), delivers messages in XML format via a buslike system using transmission control protocol connections or shared memory. A dedicated server dispatches TiD messages to distributed or local clients. The TiD message is designed to be flexible and contains time stamps for event synchronization, whereas events describe incidents, which occur during an experiment. TiD was tested extensively toward stability and latency. The effect of an occurring event jitter was analyzed and benchmarked on a reference implementation under different conditions as gigabit and 100-Mb Ethernet or Wi-Fi with a different number of event receivers. A 3-dB signal attenuation, which occurs when averaging jitter influenced trials aligned by events, is starting to become visible at around 1-2 kHz in the case of a gigabit connection. Mean event distribution times across operating systems are ranging from 0.3 to 0.5ms for a gigabit network connection for 10 6 events. Results for other environmental conditions are available in this paper. References already using TiD for event distribution are provided showing the applicability of TiD for event delivery with distributed or local clients.

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

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

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

MPEG-7 audio-visual indexing test-bed for video retrieval

NASA Astrophysics Data System (ADS)

Gagnon, Langis; Foucher, Samuel; Gouaillier, Valerie; Brun, Christelle; Brousseau, Julie; Boulianne, Gilles; Osterrath, Frederic; Chapdelaine, Claude; Dutrisac, Julie; St-Onge, Francis; Champagne, Benoit; Lu, Xiaojian

2003-12-01

This paper reports on the development status of a Multimedia Asset Management (MAM) test-bed for content-based indexing and retrieval of audio-visual documents within the MPEG-7 standard. The project, called "MPEG-7 Audio-Visual Document Indexing System" (MADIS), specifically targets the indexing and retrieval of video shots and key frames from documentary film archives, based on audio-visual content like face recognition, motion activity, speech recognition and semantic clustering. The MPEG-7/XML encoding of the film database is done off-line. The description decomposition is based on a temporal decomposition into visual segments (shots), key frames and audio/speech sub-segments. The visible outcome will be a web site that allows video retrieval using a proprietary XQuery-based search engine and accessible to members at the Canadian National Film Board (NFB) Cineroute site. For example, end-user will be able to ask to point on movie shots in the database that have been produced in a specific year, that contain the face of a specific actor who tells a specific word and in which there is no motion activity. Video streaming is performed over the high bandwidth CA*net network deployed by CANARIE, a public Canadian Internet development organization.

Aircraft

DTIC Science & Technology

2003-01-01

xml Internet . Teal Group Corp. Aviation Week and Space Technology , 18 March 2003, 1. 62 Babak Minovi, “Turbine Industry Struggles with Weak Markets ...xml Internet . Teal Group Corp. Aviation Week and Space Technology , 18 March 2003, 1. 64 Babak Minovi, “Turbine Industry Struggles with Weak Markets ...what several executives referred to as the “perfect storm” now blowing through the aviation market . With this information many questions remain: Will

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

2015-01-01

Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. PMID:26023286

Comparing Emerging XML Based Formats from a Multi-discipline Perspective

NASA Astrophysics Data System (ADS)

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.

State of the art techniques for preservation and reuse of hard copy electrocardiograms.

PubMed

Lobodzinski, Suave M; Teppner, Ulrich; Laks, Michael

2003-01-01

Baseline examinations and periodic reexaminations in longitudinal population studies, together with ongoing surveillance for morbidity and mortality, provide unique opportunities for seeking ways to enhance the value of electrocardiography (ECG) as an inexpensive and noninvasive tool for prognosis and diagnosis. We used newly developed optical ECG waveform recognition (OEWR) technique capable of extracting raw waveform data from legacy hard copy ECG recording. Hardcopy ECG recordings were scanned and processed by the OEWR algorithm. The extracted ECG datasets were formatted into a newly proposed, vendor-neutral, ECG XML data format. Oracle database was used as a repository for ECG records in XML format. The proposed technique for XML encapsulation of OEWR processed hard copy records resulted in an efficient method for inclusion of paper ECG records into research databases, thus providing their preservation, reuse and accession.

Clustering XML Documents Using Frequent Subtrees

NASA Astrophysics Data System (ADS)

Kutty, Sangeetha; Tran, Tien; Nayak, Richi; Li, Yuefeng

This paper presents an experimental study conducted over the INEX 2008 Document Mining Challenge corpus using both the structure and the content of XML documents for clustering them. The concise common substructures known as the closed frequent subtrees are generated using the structural information of the XML documents. The closed frequent subtrees are then used to extract the constrained content from the documents. A matrix containing the term distribution of the documents in the dataset is developed using the extracted constrained content. The k-way clustering algorithm is applied to the matrix to obtain the required clusters. In spite of the large number of documents in the INEX 2008 Wikipedia dataset, the proposed frequent subtree-based clustering approach was successful in clustering the documents. This approach significantly reduces the dimensionality of the terms used for clustering without much loss in accuracy.

DigitalHuman (DH): An Integrative Mathematical Model ofHuman Physiology

NASA Technical Reports Server (NTRS)

Hester, Robert L.; Summers, Richard L.; lIescu, Radu; Esters, Joyee; Coleman, Thomas G.

2010-01-01

Mathematical models and simulation are important tools in discovering the key causal relationships governing physiological processes and improving medical intervention when physiological complexity is a central issue. We have developed a model of integrative human physiology called DigitalHuman (DH) consisting of -5000 variables modeling human physiology describing cardiovascular, renal, respiratory, endocrine, neural and metabolic physiology. Users can view time-dependent solutions and interactively introduce perturbations by altering numerical parameters to investigate new hypotheses. The variables, parameters and quantitative relationships as well as all other model details are described in XML text files. All aspects of the model, including the mathematical equations describing the physiological processes are written in XML open source, text-readable files. Model structure is based upon empirical data of physiological responses documented within the peer-reviewed literature. The model can be used to understand proposed physiological mechanisms and physiological interactions that may not be otherwise intUitively evident. Some of the current uses of this model include the analyses of renal control of blood pressure, the central role of the liver in creating and maintaining insulin resistance, and the mechanisms causing orthostatic hypotension in astronauts. Additionally the open source aspect of the modeling environment allows any investigator to add detailed descriptions of human physiology to test new concepts. The model accurately predicts both qualitative and more importantly quantitative changes in clinically and experimentally observed responses. DigitalHuman provides scientists a modeling environment to understand the complex interactions of integrative physiology. This research was supported by.NIH HL 51971, NSF EPSCoR, and NASA

Improving Interoperability by Incorporating UnitsML Into Markup Languages

PubMed Central

Celebi, Ismet; Dragoset, Robert A.; Olsen, Karen J.; Schaefer, Reinhold; Kramer, Gary W.

2010-01-01

Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this “scientific meta-data” and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML—a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML. PMID:27134778

Improving Interoperability by Incorporating UnitsML Into Markup Languages.

PubMed

Celebi, Ismet; Dragoset, Robert A; Olsen, Karen J; Schaefer, Reinhold; Kramer, Gary W

2010-01-01

Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this "scientific meta-data" and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML-a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML.

Client-Server Connection Status Monitoring Using Ajax Push Technology

NASA Technical Reports Server (NTRS)

Lamongie, Julien R.

2008-01-01

This paper describes how simple client-server connection status monitoring can be implemented using Ajax (Asynchronous JavaScript and XML), JSF (Java Server Faces) and ICEfaces technologies. This functionality is required for NASA LCS (Launch Control System) displays used in the firing room for the Constellation project. Two separate implementations based on two distinct approaches are detailed and analyzed.

Evaluating the Informative Quality of Documents in SGML Format from Judgements by Means of Fuzzy Linguistic Techniques Based on Computing with Words.

ERIC Educational Resources Information Center

Herrera-Viedma, Enrique; Peis, Eduardo

2003-01-01

Presents a fuzzy evaluation method of SGML documents based on computing with words. Topics include filtering the amount of information available on the Web to assist users in their search processes; document type definitions; linguistic modeling; user-system interaction; and use with XML and other markup languages. (Author/LRW)

Architectural Design Document for the Technology Demonstration of the Joint Network Defence and Management System (JNDMS) Project

DTIC Science & Technology

2009-09-21

specified by contract no. W7714-040875/001/SV. This document contains the design of the JNDMS software to the system architecture level. Other...alternative for the presentation functions. ASP, Java, ActiveX , DLL, HTML, DHTML, SOAP, .NET HTML, DHTML, XML, Jscript, VBScript, SOAP, .NET...retrieved through the network, typically by a network management console. Information is contained in a Management Information Base (MIB), which is a data

A Digital Broadcast Item (DBI) enabling metadata repository for digital, interactive television (digiTV) feedback channel networks

NASA Astrophysics Data System (ADS)

Lugmayr, Artur R.; Mailaparampil, Anurag; Tico, Florina; Kalli, Seppo; Creutzburg, Reiner

2003-01-01

Digital television (digiTV) is an additional multimedia environment, where metadata is one key element for the description of arbitrary content. This implies adequate structures for content description, which is provided by XML metadata schemes (e.g. MPEG-7, MPEG-21). Content and metadata management is the task of a multimedia repository, from which digiTV clients - equipped with an Internet connection - can access rich additional multimedia types over an "All-HTTP" protocol layer. Within this research work, we focus on conceptual design issues of a metadata repository for the storage of metadata, accessible from the feedback channel of a local set-top box. Our concept describes the whole heterogeneous life-cycle chain of XML metadata from the service provider to the digiTV equipment, device independent representation of content, accessing and querying the metadata repository, management of metadata related to digiTV, and interconnection of basic system components (http front-end, relational database system, and servlet container). We present our conceptual test configuration of a metadata repository that is aimed at a real-world deployment, done within the scope of the future interaction (fiTV) project at the Digital Media Institute (DMI) Tampere (www.futureinteraction.tv).

A Non-technical User-Oriented Display Notation for XACML Conditions

NASA Astrophysics Data System (ADS)

Stepien, Bernard; Felty, Amy; Matwin, Stan

Ideally, access control to resources in complex IT systems ought to be handled by business decision makers who own a given resource (e.g., the pay and benefits section of an organization should decide and manage the access rules to the payroll system). To make this happen, the security and database communities need to develop vendor-independent access management tools, useable by decision makers, rather than technical personnel detached from a given business function. We have developed and implemented such tool, based on XACML. The XACML is an important emerging tool for managing complex access control applications. As a formal notation, based on an XML schema representing the grammar of a given application, XACML is precise and non-ambiguous. But this very property puts it out of reach of non-technical users. We propose a new notation for displaying and editing XACML rules that is independent of XML, and we develop an editor for it. Our notation combines a tree representation of logical expressions with an accessible natural language layer. Our early experience indicates that such rules can be grasped by non-technical users wishing to develop and control rules for accessing their own resources.

Concept-based query language approach to enterprise information systems

NASA Astrophysics Data System (ADS)

Niemi, Timo; Junkkari, Marko; Järvelin, Kalervo

2014-01-01

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

Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN

PubMed Central

Pound, Michael P.; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Leitner, Daniel; Meunier, Félicien; Pridmore, Tony P.; Schnepf, Andrea

2015-01-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. PMID:25614065

Root system markup language: toward a unified root architecture description language.

PubMed

Lobet, Guillaume; Pound, Michael P; Diener, Julien; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Javaux, Mathieu; Leitner, Daniel; Meunier, Félicien; Nacry, Philippe; Pridmore, Tony P; Schnepf, Andrea

2015-03-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. © 2015 American Society of Plant Biologists. All Rights Reserved.

XTCE: XML Telemetry and Command Exchange Tutorial, XTCE Version 1

NASA Technical Reports Server (NTRS)

Rice, Kevin; Kizzort, Brad

2008-01-01

These presentation slides are a tutorial on XML Telemetry and Command Exchange (XTCE). The goal of XTCE is to provide an industry standard mechanism for describing telemetry and command streams (particularly from satellites.) it wiill lower cost and increase validation over traditional formats, and support exchange or native format.XCTE is designed to describe bit streams, that are typical of telemetry and command in the historic space domain.

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

DTIC Science & Technology

2006-06-01

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

Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

PubMed

Holliday, Gemma L; Murray-Rust, Peter; Rzepa, Henry S

2006-01-01

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan

PubMed Central

Kinjo, Akira R.; Yamashita, Reiko; Nakamura, Haruki

2010-01-01

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/ PMID:20798081

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

PubMed

Kinjo, Akira R; Yamashita, Reiko; Nakamura, Haruki

2010-08-25

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. Database URL: http://www.pdbj.org/

ISO, FGDC, DIF and Dublin Core - Making Sense of Metadata Standards for Earth Science Data

NASA Astrophysics Data System (ADS)

Jones, P. R.; Ritchey, N. A.; Peng, G.; Toner, V. A.; Brown, H.

2014-12-01

Metadata standards provide common definitions of metadata fields for information exchange across user communities. Despite the broad adoption of metadata standards for Earth science data, there are still heterogeneous and incompatible representations of information due to differences between the many standards in use and how each standard is applied. Federal agencies are required to manage and publish metadata in different metadata standards and formats for various data catalogs. In 2014, the NOAA National Climatic data Center (NCDC) managed metadata for its scientific datasets in ISO 19115-2 in XML, GCMD Directory Interchange Format (DIF) in XML, DataCite Schema in XML, Dublin Core in XML, and Data Catalog Vocabulary (DCAT) in JSON, with more standards and profiles of standards planned. Of these standards, the ISO 19115-series metadata is the most complete and feature-rich, and for this reason it is used by NCDC as the source for the other metadata standards. We will discuss the capabilities of metadata standards and how these standards are being implemented to document datasets. Successful implementations include developing translations and displays using XSLTs, creating links to related data and resources, documenting dataset lineage, and establishing best practices. Benefits, gaps, and challenges will be highlighted with suggestions for improved approaches to metadata storage and maintenance.

Combining dictionary techniques with extensible markup language (XML)--requirements to a new approach towards flexible and standardized documentation.

PubMed Central

Altmann, U.; Tafazzoli, A. G.; Noelle, G.; Huybrechts, T.; Schweiger, R.; Wächter, W.; Dudeck, J. W.

1999-01-01

In oncology various international and national standards exist for the documentation of different aspects of a disease. Since elements of these standards are repeated in different contexts, a common data dictionary could support consistent representation in any context. For the construction of such a dictionary existing documents have to be worked up in a complex procedure, that considers aspects of hierarchical decomposition of documents and of domain control as well as aspects of user presentation and models of the underlying model of patient data. In contrast to other thesauri, text chunks like definitions or explanations are very important and have to be preserved, since oncologic documentation often means coding and classification on an aggregate level and the safe use of coding systems is an important precondition for comparability of data. This paper discusses the potentials of the use of XML in combination with a dictionary for the promotion and development of standard conformable applications for tumor documentation. PMID:10566311

Use of standard vocabulary services in validation of water resources data

NASA Astrophysics Data System (ADS)

Yu, Jonathan; Cox, Simon; Ratcliffe, David

2010-05-01

Ontology repositories are increasingly being exposed through vocabulary and concept services. Primarily this is in support of resource discovery. Thesaurus functionality and even more sophisticated reasoning offers the possibility of overcoming the limitations of simple text-matching and tagging which is the basis of most search. However, controlled vocabularies have other important roles in distributed systems: in particular in constraining content validity. A national water information system established by the Australian Bureau of Meterorology ('the Bureau') has deployed a system for ingestion of data from multiple providers. This uses a http interface onto separately maintained vocabulary services as part of the quality assurance chain. With over 200 data providers potentially transferring data to the Bureau, a standard XML-based Water Data Transfer Format (WDTF) was developed for receipt of data into an integrated national water information system. The WDTF schema was built upon standards from the Open Geospatial Consortium (OGC). The structure and syntax specified by a W3C XML Schema is complemented by additional constraints described using Schematron. These implement important content requirements and business rules including: • Restricted cardinality: where optional elements and attributes inherited from the base standards become mandatory in the application, or repeatable elements or attributes are limited to one or omitted. For example, the sampledFeature element from O&M is optional but is mandatory for a samplingPoint element in WDTF. • Vocabulary checking: WDTF data use seventeen vocabularies or code lists derived from Regulations under the Commonwealth Water Act 2007. Examples of codelists are the Australian Water Regulations list, observed property vocabulary, and units of measures. • Contextual constraints: in many places, the permissible value is dependent on the value of another field. For example, within observations the unit of measure must be commensurate with the observed property type Validation of data submitted in WDTF uses a two-pass approach. First, syntax and structural validation is performed by standard XML Schema validation tools. Second, validation of contextual constraints and code list checking is performed using a hybrid method combining context-sensitive rule-based validation (allowing the rules to be expressed within a given context) and semantic vocabulary services. Schematron allows rules to incorporate assertions of XPath expressions to access and constrain element content, therefore enabling contextual constraints. Schematron is also used to perform element cardinality checking. The vocabularies or code lists are formalized in SKOS (Simple Knowledge Organization System), an RDF-based language. SKOS provides mechanisms to define concepts, associate them with (multi-lingual) labels or terms, and record thesaurus-like relationships between them. The vocabularies are managed in a RDF database or semantic triple store. Querying is implemented as a semantic vocabulary service, with an http-based API that allows queries to be issued from rules written in Schematron. WDTF has required development and deployment of some ontologies whose scope is much more general than this application, in particular covering 'observed properties' and 'units of measure', which also have to be related to each other and consistent with the dimensional analysis. Separation of the two validation passes reflects the separate governance and stability of the structural and content rules, and allows an organisation's business rules to be moved out of the XML schema definition and the XML schema to be reused by other businesses with their own specific rules. With the general approach proven, harmonization opportunities with more generic services are being explored, such as the GEMET API for SKOS, developed by the European Environment Agency. Acknowledgements: The authors would like to thank the AUSCOPE team for their development and support provided of the vocabulary services.

A pragmatic method for transforming clinical research data from the research electronic data capture "REDCap" to Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM): Development and evaluation of REDCap2SDTM.

PubMed

Yamamoto, Keiichi; Ota, Keiko; Akiya, Ippei; Shintani, Ayumi

2017-06-01

The Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) can be used for new drug application studies as well as secondarily for creating a clinical research data warehouse to leverage clinical research study data across studies conducted within the same disease area. However, currently not all clinical research uses Clinical Data Acquisition Standards Harmonization (CDASH) beginning in the set-up phase of the study. Once already initiated, clinical studies that have not utilized CDASH are difficult to map in the SDTM format. In addition, most electronic data capture (EDC) systems are not equipped to export data in SDTM format; therefore, in many cases, statistical software is used to generate SDTM datasets from accumulated clinical data. In order to facilitate efficient secondary use of accumulated clinical research data using SDTM, it is necessary to develop a new tool to enable mapping of information for SDTM, even during or after the clinical research. REDCap is an EDC system developed by Vanderbilt University and is used globally by over 2100 institutions across 108 countries. In this study, we developed a simulated clinical trial to evaluate a tool called REDCap2SDTM that maps information in the Field Annotation of REDCap to SDTM and executes data conversion, including when data must be pivoted to accommodate the SDTM format, dynamically, by parsing the mapping information using R. We confirmed that generating SDTM data and the define.xml file from REDCap using REDCap2SDTM was possible. Conventionally, generation of SDTM data and the define.xml file from EDC systems requires the creation of individual programs for each clinical study. However, our proposed method can be used to generate this data and file dynamically without programming because it only involves entering the mapping information into the Field Annotation, and additional data into specific files. Our proposed method is adaptable not only to new drug application studies but also to all types of research, including observational and public health studies. Our method is also adaptable to clinical data collected with CDASH at the beginning of a study in non-standard format. We believe that this tool will reduce the workload of new drug application studies and will support data sharing and reuse of clinical research data in academia. Copyright © 2017 Elsevier Inc. All rights reserved.

Innovative Technology for Teaching Introductory Astronomy

NASA Astrophysics Data System (ADS)

Guidry, Mike

The application of state-of-the-art technology (primarily Java and Flash MX Actionscript on the client side and Java PHP PERL XML and SQL databasing on the server side) to the teaching of introductory astronomy will be discussed. A completely online syllabus in introductory astronomy built around more than 350 interactive animations called ""Online Journey through Astronomy"" and a new set of 20 online virtual laboratories in astronomy that we are currently developing will be used as illustration. In addition to demonstration of the technology our experience using these technologies to teach introductory astronomy to thousands of students in settings ranging from traditional classrooms to full distance learning will be summarized. Recent experiments using Java and vector graphics programming of handheld devices (Personal Digital Assistants and cell phones) with wireless wide-area connectivity for applications in astronomy education will also be described.

A new concept of a unified parameter management, experiment control, and data analysis in fMRI: application to real-time fMRI at 3T and 7T.

PubMed

Hollmann, M; Mönch, T; Mulla-Osman, S; Tempelmann, C; Stadler, J; Bernarding, J

2008-10-30

In functional MRI (fMRI) complex experiments and applications require increasingly complex parameter handling as the experimental setup usually consists of separated soft- and hardware systems. Advanced real-time applications such as neurofeedback-based training or brain computer interfaces (BCIs) may even require adaptive changes of the paradigms and experimental setup during the measurement. This would be facilitated by an automated management of the overall workflow and a control of the communication between all experimental components. We realized a concept based on an XML software framework called Experiment Description Language (EDL). All parameters relevant for real-time data acquisition, real-time fMRI (rtfMRI) statistical data analysis, stimulus presentation, and activation processing are stored in one central EDL file, and processed during the experiment. A usability study comparing the central EDL parameter management with traditional approaches showed an improvement of the complete experimental handling. Based on this concept, a feasibility study realizing a dynamic rtfMRI-based brain computer interface showed that the developed system in combination with EDL was able to reliably detect and evaluate activation patterns in real-time. The implementation of a centrally controlled communication between the subsystems involved in the rtfMRI experiments reduced potential inconsistencies, and will open new applications for adaptive BCIs.

Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations.

PubMed

Munkhdalai, Tsendsuren; Li, Meijing; Batsuren, Khuyagbaatar; Park, Hyeon Ah; Choi, Nak Hyeon; Ryu, Keun Ho

2015-01-01

Chemical and biomedical Named Entity Recognition (NER) is an essential prerequisite task before effective text mining can begin for biochemical-text data. Exploiting unlabeled text data to leverage system performance has been an active and challenging research topic in text mining due to the recent growth in the amount of biomedical literature. We present a semi-supervised learning method that efficiently exploits unlabeled data in order to incorporate domain knowledge into a named entity recognition model and to leverage system performance. The proposed method includes Natural Language Processing (NLP) tasks for text preprocessing, learning word representation features from a large amount of text data for feature extraction, and conditional random fields for token classification. Other than the free text in the domain, the proposed method does not rely on any lexicon nor any dictionary in order to keep the system applicable to other NER tasks in bio-text data. We extended BANNER, a biomedical NER system, with the proposed method. This yields an integrated system that can be applied to chemical and drug NER or biomedical NER. We call our branch of the BANNER system BANNER-CHEMDNER, which is scalable over millions of documents, processing about 530 documents per minute, is configurable via XML, and can be plugged into other systems by using the BANNER Unstructured Information Management Architecture (UIMA) interface. BANNER-CHEMDNER achieved an 85.68% and an 86.47% F-measure on the testing sets of CHEMDNER Chemical Entity Mention (CEM) and Chemical Document Indexing (CDI) subtasks, respectively, and achieved an 87.04% F-measure on the official testing set of the BioCreative II gene mention task, showing remarkable performance in both chemical and biomedical NER. BANNER-CHEMDNER system is available at: https://bitbucket.org/tsendeemts/banner-chemdner.

Joint Battlespace Infosphere: Information Management Within a C2 Enterprise

DTIC Science & Technology

2005-06-01

using. In version 1.2, we support both MySQL and Oracle as underlying implementations where the XML metadata schema is mapped into relational tables in...Identity Servers, Role-Based Access Control, and Policy Representation – Databases: Oracle , MySQL , TigerLogic, Berkeley XML DB 15 Instrumentation Services...converted to SQL for execution. Invocations are then forwarded to the appropriate underlying IOR core components that have the responsibility of issuing

eMontage: An Architecture for Rapid Integration of Situational Awareness Data at the Edge

DTIC Science & Technology

2013-05-01

Request Response Interaction Android Client Dispatcher Servlet Spring MVC Controller Camel Producer Template Camel Route Remote Data Service - REST...8SATURN 2013© 2013 Carnegie Mellon University Publish Subscribe Interaction Android Client Dispatcher Servlet Spring MVC Controller Remote Data...set ..., "’"C oUkRelw•b J’- - ’ ~ ’~------’ ~-------- ’-------~ , Parse XML into a single Java XML Document object. -=--:=’ Software Engineering

C3I and Modelling and Simulation (M&S) Interoperability

DTIC Science & Technology

2004-03-01

customised Open Source products. The technical implementation is based on the use of the eXtendend Markup Language (XML) and Python . XML is developed...to structure, store and send information. The language is focus on the description of data. Python is a portable, interpreted, object-oriented...programming language. A huge variety of usable Open Source Projects were issued by the Python Community. 3.1 Phase 1: Feasibility Studies Phase 1 was

Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data.

PubMed

Kuhn, Stefan; Helmus, Tobias; Lancashire, Robert J; Murray-Rust, Peter; Rzepa, Henry S; Steinbeck, Christoph; Willighagen, Egon L

2007-01-01

CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist.

CrossTalk: The Journal of Defense Software Engineering. Volume 21, Number 10, October 2008

DTIC Science & Technology

2008-10-01

proprietary modeling offerings, there is considerable conver- gence around Business Process Modeling Notation ( BPMN ). The research also found strong...support across vendors for the Business Process Execution Language standard, though there is also emerging support for direct execution of BPMN through...the use of the XML Process Definition Language, an XML serialization of BPMN . Many vendors also provide the needed moni- toring of those processes at

Ordered Backward XPath Axis Processing against XML Streams

NASA Astrophysics Data System (ADS)

Nizar M., Abdul; Kumar, P. Sreenivasa

Processing of backward XPath axes against XML streams is challenging for two reasons: (i) Data is not cached for future access. (ii) Query contains steps specifying navigation to the data that already passed by. While there are some attempts to process parent and ancestor axes, there are very few proposals to process ordered backward axes namely, preceding and preceding-sibling. For ordered backward axis processing, the algorithm, in addition to overcoming the limitations on data availability, has to take care of ordering constraints imposed by these axes. In this paper, we show how backward ordered axes can be effectively represented using forward constraints. We then discuss an algorithm for XML stream processing of XPath expressions containing ordered backward axes. The algorithm uses a layered cache structure to systematically accumulate query results. Our experiments show that the new algorithm gains remarkable speed up over the existing algorithm without compromising on bufferspace requirement.

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

Bottom-Up Evaluation of Twig Join Pattern Queries in XML Document Databases

NASA Astrophysics Data System (ADS)

Chen, Yangjun

Since the extensible markup language XML emerged as a new standard for information representation and exchange on the Internet, the problem of storing, indexing, and querying XML documents has been among the major issues of database research. In this paper, we study the twig pattern matching and discuss a new algorithm for processing ordered twig pattern queries. The time complexity of the algorithmis bounded by O(|D|·|Q| + |T|·leaf Q ) and its space overhead is by O(leaf T ·leaf Q ), where T stands for a document tree, Q for a twig pattern and D is a largest data stream associated with a node q of Q, which contains the database nodes that match the node predicate at q. leaf T (leaf Q ) represents the number of the leaf nodes of T (resp. Q). In addition, the algorithm can be adapted to an indexing environment with XB-trees being used.

A Simple XML Producer-Consumer Protocol

NASA Technical Reports Server (NTRS)

Smith, Warren; Gunter, Dan; Quesnel, Darcy

2000-01-01

This document describes a simple XML-based protocol that can be used for producers of events to communicate with consumers of events. The protocol described here is not meant to be the most efficient protocol, the most logical protocol, or the best protocol in any way. This protocol was defined quickly and it's intent is to give us a reasonable protocol that we can implement relatively easily and then use to gain experience in distributed event services. This experience will help us evaluate proposals for event representations, XML-based encoding of information, and communication protocols. The next section of this document describes how we represent events in this protocol and then defines the two events that we choose to use for our initial experiments. These definitions are made by example so that they are informal and easy to understand. The following section then proceeds to define the producer-consumer protocol we have agreed upon for our initial experiments.

Techniques for integrating ‐omics data

PubMed Central

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present ‐omics community, because ‐omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data. PMID:19255651

Techniques for integrating -omics data.

PubMed

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.

Informal information for web-based engineering catalogues

NASA Astrophysics Data System (ADS)

Allen, Richard D.; Culley, Stephen J.; Hicks, Ben J.

2001-10-01

Success is highly dependent on the ability of a company to efficiently produce optimal designs. In order to achieve this companies must minimize time to market and possess the ability to make fully informed decisions at the early phase of the design process. Such decisions may include the choice of component and suppliers, as well as cost and maintenance considerations. Computer modeling and electronic catalogues are becoming the preferred medium for the selection and design of mechanical components. In utilizing these techniques, the designer demands the capability to identify, evaluate and select mechanical components both quantitatively and qualitatively. Quantitative decisions generally encompass performance data included in the formal catalogue representation. It is in the area of qualitative decisions that the use of what the authors call 'Informal Information' is of crucial importance. Thus, 'Informal Information' must often be incorporated into the selection process and selection systems. This would enable more informed decisions to be made quicker, without the need for information retrieval via discussion with colleagues in the design environment. This paper provides an overview of the use of electronic information in the design of mechanical systems, including a discussion of limitations of current technology. The importance of Informal Information is discussed and the requirements for association with web based electronic catalogues are developed. This system is based on a flexible XML schema and enables the storage, classification and recall of Informal Information packets. Furthermore, a strategy for the inclusion of Informal Information is proposed, and an example case is used to illustrate the benefits.

Benefits to the Simulation Training Community of a New ANSI Standard for the Exchange of Aero Simulation Models

NASA Technical Reports Server (NTRS)

Hildreth, Bruce L.; Jackson, E. Bruce

2009-01-01

The American Institute of Aeronautics Astronautics (AIAA) Modeling and Simulation Technical Committee is in final preparation of a new standard for the exchange of flight dynamics models. The standard will become an ANSI standard and is under consideration for submission to ISO for acceptance by the international community. The standard has some a spects that should provide benefits to the simulation training community. Use of the new standard by the training simulation community will reduce development, maintenance and technical refresh investment on each device. Furthermore, it will significantly lower the cost of performing model updates to improve fidelity or expand the envelope of the training device. Higher flight fidelity should result in better transfer of training, a direct benefit to the pilots under instruction. Costs of adopting the standard are minimal and should be paid back within the cost of the first use for that training device. The standard achie ves these advantages by making it easier to update the aerodynamic model. It provides a standard format for the model in a custom eXtensible Markup Language (XML) grammar, the Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML). It employs an existing XML grammar, MathML, to describe the aerodynamic model in an input data file, eliminating the requirement for actual software compilation. The major components of the aero model become simply an input data file, and updates are simply new XML input files. It includes naming and axis system conventions to further simplify the exchange of information.

CytometryML binary data standards

NASA Astrophysics Data System (ADS)

Leif, Robert C.

2005-03-01

CytometryML is a proposed new Analytical Cytology (Cytomics) data standard, which is based on a common set of XML schemas for encoding flow cytometry and digital microscopy text based data types (metadata). CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. The separation of the large binary data objects (list mode and image data) from the XML description of the metadata permits the metadata to be directly displayed, analyzed, and reported with standard commercial software packages; the direct use of XML languages; and direct interfacing with clinical information systems. The separation of the binary data into its own files simplifies parsing because all extraneous header data has been eliminated. The storage of images as two-dimensional arrays without any extraneous data, such as in the Adobe Photoshop RAW format, facilitates the development by scientists of their own analysis and visualization software. Adobe Photoshop provided the display infrastructure and the translation facility to interconvert between the image data from commercial formats and RAW format. Similarly, the storage and parsing of list mode binary data type with a group of parameters that are specified at compilation time is straight forward. However when the user is permitted at run-time to select a subset of the parameters and/or specify results of mathematical manipulations, the development of special software was required. The use of CytometryML will permit investigators to be able to create their own interoperable data analysis software and to employ commercially available software to disseminate their data.

Knowledge-Centric Management of Business Rules in a Pharmacy

NASA Astrophysics Data System (ADS)

Puustjärvi, Juha; Puustjärvi, Leena

A business rule defines or constraints some aspect of the business. In healthcare sector many of the business rules are dictated by law or medical regulations, which are constantly changing. This is a challenge for the healthcare organizations. Although there is available several commercial business rule management systems the problem from pharmacies point of view is that these systems are overly geared towards the automation and manipulation of business rules, while the main need in pharmacies lies in easy retrieving of business rules within daily routines. Another problem is that business rule management systems are isolated in the sense that they have their own data stores that cannot be accessed by other information systems used in pharmacies. As a result, a pharmacist is burdened by accessing many systems inside a user task. In order to avoid this problem we have modeled business rules as well as their relationships to other relevant information by OWL (Web Ontology Language) such that the ontology is shared among the pharmacy's applications. In this way we can avoid the problems of isolated applications and replicated data. The ontology also encourages pharmacies business agility, i.e., the ability to react more rapidly to the changes required by the new business rules. The deployment of the ontology requires that stored business rules are annotated by appropriate metadata descriptions, which are presented by RDF/XML serialization format. However, neither the designer nor the pharmacists are burdened by RDF/XML format as there are sophisticated graphical editors that can be used.

Design of an eMonitor system to transport electronic patient care report (ePCR) information in unstable MobileIP wireless environment.

PubMed

Giovanni, Mazza G; Shenvi, Rohit; Battles, Marcie; Orthner, Helmuth F

2008-11-06

The eMonitor is a component of the ePatient system; a prototype system used by emergency medical services (EMS) personnel in the field to record and transmits electronic patient care report (ePCR) information interactively. The eMonitor component allows each Mobile Data Terminal (MDT) on an unreliable Cisco MobileIP wireless network to securely send and received XML messages used to update patient information to and from the MDT before, during and after the transport of a patient.

Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation

NASA Technical Reports Server (NTRS)

Afjeh, Abdollah A.; Reed, John A.

2003-01-01

The following reports are presented on this project:A first year progress report on: Development of a Dynamically Configurable,Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; A second year progress report on: Development of a Dynamically Configurable, Object-Oriented Framework for Distributed, Multi-modal Computational Aerospace Systems Simulation; An Extensible, Interchangeable and Sharable Database Model for Improving Multidisciplinary Aircraft Design; Interactive, Secure Web-enabled Aircraft Engine Simulation Using XML Databinding Integration; and Improving the Aircraft Design Process Using Web-based Modeling and Simulation.

Quantum simulation of disordered systems with cold atoms

NASA Astrophysics Data System (ADS)

Garreau, Jean-Claude

2017-01-01

This paper reviews the physics of quantum disorder in relation with a series of experiments using laser-cooled atoms exposed to "kicks" of a standing wave, realizing a paradigmatic model of quantum chaos, the kicked rotor. This dynamical system can be mapped onto a tight-binding Hamiltonian with pseudo-disorder, formally equivalent to the Anderson model of quantum disorder, with quantum chaos playing the role of disorder. This provides a very good quantum simulator for the Anderson physics. xml:lang="fr"

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

VIDANN: a video annotation system.

PubMed

De Clercq, A; Buysse, A; Roeyers, H; Ickes, W; Ponnet, K; Verhofstadt, L

2001-05-01

VIDANN is a computer program that allows participants to watch a video on a standard TV and to write their annotations (thought/feeling entries) on paper attached to a writing tablet. The system is designed as a Microsoft ActiveX module. It can be further adapted by the individual researcher through the use of a VBScript. All data, including the participant's handwriting, are stored in an XML database. An accompanying Wizard has been designed that enables researchers to generate VBScripts for standard configurations.

OTF CCSDS Mission Operations Prototype. Directory and Action Service. Phase I: Exit Presentation

NASA Technical Reports Server (NTRS)

Reynolds, Walter F.; Lucord, Steven A.; Stevens, John E.

2009-01-01

This slide presentation describes the phase I directory and action service prototype for the CCSDS system. The project goals are to: (1) Demonstrate the use of Mission Operations standards to implement Directory and Action Services (2) Investigate Mission Operations language neutrality (3) Investigate C3I XML interoperability concepts (4) Integrate applicable open source technologies in a Service Oriented Architecture

The stochastic energy-Casimir method

NASA Astrophysics Data System (ADS)

Arnaudon, Alexis; Ganaba, Nader; Holm, Darryl D.

2018-04-01

In this paper, we extend the energy-Casimir stability method for deterministic Lie-Poisson Hamiltonian systems to provide sufficient conditions for stability in probability of stochastic dynamical systems with symmetries. We illustrate this theory with classical examples of coadjoint motion, including the rigid body, the heavy top, and the compressible Euler equation in two dimensions. The main result is that stable deterministic equilibria remain stable in probability up to a certain stopping time that depends on the amplitude of the noise for finite-dimensional systems and on the amplitude of the spatial derivative of the noise for infinite-dimensional systems. xml:lang="fr"

An Approach for Implementation of Project Management Information Systems

NASA Astrophysics Data System (ADS)

Běrziša, Solvita; Grabis, Jānis

Project management is governed by project management methodologies, standards, and other regulatory requirements. This chapter proposes an approach for implementing and configuring project management information systems according to requirements defined by these methodologies. The approach uses a project management specification framework to describe project management methodologies in a standardized manner. This specification is used to automatically configure the project management information system by applying appropriate transformation mechanisms. Development of the standardized framework is based on analysis of typical project management concepts and process and existing XML-based representations of project management. A demonstration example of project management information system's configuration is provided.

C2 Product-Centric Approach to Transforming Current C4ISR Information Architectures

DTIC Science & Technology

2004-06-01

each type of environment . For “Cultural Feature” Entity Kind only the “Land” Domain is defined and for “ Environmental ” Entity Kind only the...take advantage of both worlds. In particular, the unifying concept of a Model-Driven Architecture (MDA) under development by the Object Management...Exchange Requirements (IER) to an XML environment . FCS [4] developers have embraced both UML and XML for their architectures and MIP [5] too is migrating

Leveraging Small-Lexicon Language Models

DTIC Science & Technology

2016-12-31

shown in Figure 1. This “easy to use” XML build (from a lexicon.xml file) bakes in source and language metadata, shows both raw (“copper”) and...requires it (e.g. used as standoff annotation), or some or all metadata can be baked into each and every set. Please let us know if a custom...interpretations are plausible, they are pipe-separated: bake #v#1|toast#v#1. • several word classes have been added (with all items numbered #1): d

Internet Economics IV

DTIC Science & Technology

2004-08-01

components, and B2B /B2C aspects of those in a technical and economic snapshot. Talk number six discusses the trade-off between quality and cost, which...web services have been defined. The fifth talk summarizes key aspects of XML (Extended Markup Language), Web Services and their components, and B2B ...Internet is Run: A Worldwide Perspective 69 Christoph Pauls 5 XML, Web Services and B2C/ B2B : A Technical and Economical Snap- shot 87 Matthias Pitt 6

Design and implementation of the mobility assessment tool: software description.

PubMed

Barnard, Ryan T; Marsh, Anthony P; Rejeski, Walter Jack; Pecorella, Anthony; Ip, Edward H

2013-07-23

In previous work, we described the development of an 81-item video-animated tool for assessing mobility. In response to criticism levied during a pilot study of this tool, we sought to develop a new version built upon a flexible framework for designing and administering the instrument. Rather than constructing a self-contained software application with a hard-coded instrument, we designed an XML schema capable of describing a variety of psychometric instruments. The new version of our video-animated assessment tool was then defined fully within the context of a compliant XML document. Two software applications--one built in Java, the other in Objective-C for the Apple iPad--were then built that could present the instrument described in the XML document and collect participants' responses. Separating the instrument's definition from the software application implementing it allowed for rapid iteration and easy, reliable definition of variations. Defining instruments in a software-independent XML document simplifies the process of defining instruments and variations and allows a single instrument to be deployed on as many platforms as there are software applications capable of interpreting the instrument, thereby broadening the potential target audience for the instrument. Continued work will be done to further specify and refine this type of instrument specification with a focus on spurring adoption by researchers in gerontology and geriatric medicine.

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

PubMed

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/.

Design and implementation of the mobility assessment tool: software description

PubMed Central

2013-01-01

Background In previous work, we described the development of an 81-item video-animated tool for assessing mobility. In response to criticism levied during a pilot study of this tool, we sought to develop a new version built upon a flexible framework for designing and administering the instrument. Results Rather than constructing a self-contained software application with a hard-coded instrument, we designed an XML schema capable of describing a variety of psychometric instruments. The new version of our video-animated assessment tool was then defined fully within the context of a compliant XML document. Two software applications—one built in Java, the other in Objective-C for the Apple iPad—were then built that could present the instrument described in the XML document and collect participants’ responses. Separating the instrument’s definition from the software application implementing it allowed for rapid iteration and easy, reliable definition of variations. Conclusions Defining instruments in a software-independent XML document simplifies the process of defining instruments and variations and allows a single instrument to be deployed on as many platforms as there are software applications capable of interpreting the instrument, thereby broadening the potential target audience for the instrument. Continued work will be done to further specify and refine this type of instrument specification with a focus on spurring adoption by researchers in gerontology and geriatric medicine. PMID:23879716

A Recipe for Streamlining Mission Management

NASA Technical Reports Server (NTRS)

Mitchell, Andrew E.; Semancik, Susan K.

2004-01-01

This paper describes a project's design and implementation for streamlining mission management with knowledge capture processes across multiple organizations of a NASA directorate. Thc project's focus is on standardizing processes and reports; enabling secure information access and case of maintenance; automating and tracking appropriate workflow rules through process mapping; and infusing new technologies. This paper will describe a small team's experiences using XML technologies through an enhanced vendor suite of applications integrated on Windows-based platforms called the Wallops Integrated Scheduling and Document Management System (WISDMS). This paper describes our results using this system in a variety of endeavors, including providing range project scheduling and resource management for a Range and Mission Management Office; implementing an automated Customer Feedback system for a directorate; streamlining mission status reporting across a directorate; and initiating a document management, configuration management and portal access system for a Range Safety Office's programs. The end result is a reduction of the knowledge gap through better integration and distribution of information, improved process performance, automated metric gathering, and quicker identification of problem areas and issues. However, the real proof of the pudding comes through overcoming the user's reluctance to replace familiar, seasoned processes with new technology ingredients blended with automated procedures in an untested recipe. This paper shares some of the team's observations that led to better implementation techniques, as well as an IS0 9001 Best Practices citation. This project has provided a unique opportunity to advance NASA's competency in new technologies, as well as to strategically implement them within an organizational structure, while wetting the appetite for continued improvements in mission management.

Islandora A Flexible Drupal-Based Virtual Research Environment

NASA Astrophysics Data System (ADS)

Leggott, M.; Pan, J.

2011-12-01

Research today exists in a landscape where data flood in, literature grows exponentially, and disciplinary boundaries are increasingly porous. Many of the greatest challenges facing researchers are related to managing the information produced during the research life cycle - from the discussion of new projects to the creation of funding proposals, the production and analysis of data, and the presentation of findings via conferences and scholarly publications. The Islandora framework provides a system that stewards digital data in any form (textual, numeric, scientific, multimedia) along the entire course of this research continuum, it facilitates collaboration not just among physically distant members of research groups but also among research groups and their associated support groups. Because Islandora accommodates both the project-specific, experiment-based context and the cross-project, interdisciplinary exploration context of data, the approach to the creation and discovery of data can be called 'discipline-agnostic.' UPEI's Virtual Research Environment (or VRE) has demonstrated the immense benefits of such an approach. In one example scientists collects samples, create detailed metadata for each sample, potentially generating thousands of data files of various kinds, which can all be loaded in one step. Software (some of it developed specifically for this project) then combines, recombines, and transforms these data into alternate formats for analysis -- thereby saving scientists hundreds of hours of manual labor. Wherever possible data are translated, converting them from proprietary file formats to standard XML, and stored -- thereby exposing the data to a larger audience that may bring them together with quite different samples or experiments in novel ways. The same computer processes and software work-flows brought to bear in the context of one research program can be re-used in other areas and across completely different disciplines, since the data are represented by similar streams of bits and bytes. Islandora is developing a strong set of features of interest to the geoscience community, including: a generic XML form builder with current support for DC, FGDC, EML, KML, NCD, Darwin Core, DDI, PREMIS and more coming). Strong support for large image files via JPEG2000, document formats, entity extraction, geo-referencing functions, OpenLayers integration, mobile iPad/iPhone interfaces and more make Islandora an ideal digital asset management system for geoscience researchers. Islandora is an open source project developed at the University of PEI, with a full suite of services available from the UPEI spin-off DiscoveryGarden Inc. Islandora is built around the Drupal content management system and the Fedora repository, providing a robust and flexible digital asset management framework. Examples of Islandora systems include a variety of research data repositories, including some examples in the earth sciences, such as the ESDORA system at Oak Ridge National Laboratory. The system will be described in detail, using a number of research systems as examples.

An Observation Knowledgebase for Hinode Data

NASA Astrophysics Data System (ADS)

Hurlburt, Neal E.; Freeland, S.; Green, S.; Schiff, D.; Seguin, R.; Slater, G.; Cirtain, J.

2007-05-01

We have developed a standards-based system for the Solar Optical and X Ray Telescopes on the Hinode orbiting solar observatory which can serve as part of a developing Heliophysics informatics system. Our goal is to make the scientific data acquired by Hinode more accessible and useful to scientists by allowing them to do reasoning and flexible searches on observation metadata and to ask higher-level questions of the system than previously allowed. The Hinode Observation Knowledgebase relates the intentions and goals of the observation planners (as-planned metadata) with actual observational data (as-run metadata), along with connections to related models, data products and identified features (follow-up metadata) through a citation system. Summaries of the data (both as image thumbnails and short "film strips") serve to guide researchers to the observations appropriate for their research, and these are linked directly to the data catalog for easy extraction and delivery. The semantic information of the observation (Field of view, wavelength, type of observable, average cadence etc.) is captured through simple user interfaces and encoded using the VOEvent XML standard (with the addition of some solar-related extensions). These interfaces merge metadata acquired automatically during both mission planning and an data analysis (see Seguin et. al. 2007 at this meeting) phases with that obtained directly from the planner/analyst and send them to be incorporated into the knowledgebase. The resulting information is automatically rendered into standard categories based on planned and recent observations, as well as by popularity and recommendations by the science team. They are also directly searchable through both and web-based searches and direct calls to the API. Observations details can also be rendered as RSS, iTunes and Google Earth interfaces. The resulting system provides a useful tool to researchers and can act as a demonstration for larger, more complex systems.

Tactical Web Services: Using XML and Java Web Services to Conduct Real-Time Net-Centric Sonar Visualization

DTIC Science & Technology

2004-09-01

Rosetti USN U.S. Navy Chesterton, IN 6. Erik Chaum NUWC Newport, RI 7. David Bellino NPRI Newport, RI 8. Dick Nadolink NUWC Newport, RI...found at (http://www.parallelgraphics.com/products/cortona). G. JFREECHART JFreeChart is an open source Java API created by David Gilbert and...www.xj3d.org/. Accessed 3 September 2004. Hunter, David , Kurt Cagle, and Chris Dix, eds. Beginning XML, Second Edition. Indianapolis, IN

2035 Air Dominance Requirements for State-On-State Conflict

DTIC Science & Technology

2011-02-16

story.jsp?id=news/ awst /2011/01/10/AW_01_10_ 2011_p58-280833.xml&channel=misc (accessed 3 Jan 2011). Bilbro, James. “Technology Readiness Levels.” JB...channel = awst &id =news/aw121508p2.xml&headline=null&prev=10. (accessed 3 January 2011). Global Security.org. “Miniature Air-Launched Decoy (MALD...Battle.” Center for Strategic and Budgetary Assessment, http://www.csba online.com/4Publications/PubLibrary/ R .20100518.Slides_AirSea_Batt/ R .20100518

Generating GraphML XML Files for Graph Visualization of Architectures and Event Traces for the Monterey Phoenix Program

DTIC Science & Technology

2012-09-01

Thesis Advisor: Mikhail Auguston Second Reader: Terry Norbraten THIS PAGE INTENTIONALLY LEFT BLANK i REPORT DOCUMENTATION PAGE Form Approved...Language (GraphML). MPGrapher compiles well- formed XML files that conform to the yEd GraphML schema. These files will be opened and analyzed using...ABSTRACT UU NSN 7540-01-280-5500 Standard Form 298 (Rev. 2-89) Prescribed by ANSI Std. 239-18 ii THIS PAGE INTENTIONALLY LEFT BLANK iii Approved

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Pragmatic Metadata Management for Integration into Multiple Spatial Data Infrastructure Systems and Platforms

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Scott, S.

2013-12-01

While there has been a convergence towards a limited number of standards for representing knowledge (metadata) about geospatial (and other) data objects and collections, there exist a variety of community conventions around the specific use of those standards and within specific data discovery and access systems. This combination of limited (but multiple) standards and conventions creates a challenge for system developers that aspire to participate in multiple data infrastrucutres, each of which may use a different combination of standards and conventions. While Extensible Markup Language (XML) is a shared standard for encoding most metadata, traditional direct XML transformations (XSLT) from one standard to another often result in an imperfect transfer of information due to incomplete mapping from one standard's content model to another. This paper presents the work at the University of New Mexico's Earth Data Analysis Center (EDAC) in which a unified data and metadata management system has been developed in support of the storage, discovery and access of heterogeneous data products. This system, the Geographic Storage, Transformation and Retrieval Engine (GSTORE) platform has adopted a polyglot database model in which a combination of relational and document-based databases are used to store both data and metadata, with some metadata stored in a custom XML schema designed as a superset of the requirements for multiple target metadata standards: ISO 19115-2/19139/19110/19119, FGCD CSDGM (both with and without remote sensing extensions) and Dublin Core. Metadata stored within this schema is complemented by additional service, format and publisher information that is dynamically "injected" into produced metadata documents when they are requested from the system. While mapping from the underlying common metadata schema is relatively straightforward, the generation of valid metadata within each target standard is necessary but not sufficient for integration into multiple data infrastructures, as has been demonstrated through EDAC's testing and deployment of metadata into multiple external systems: Data.Gov, the GEOSS Registry, the DataONE network, the DSpace based institutional repository at UNM and semantic mediation systems developed as part of the NASA ACCESS ELSeWEB project. Each of these systems requires valid metadata as a first step, but to make most effective use of the delivered metadata each also has a set of conventions that are specific to the system. This presentation will provide an overview of the underlying metadata management model, the processes and web services that have been developed to automatically generate metadata in a variety of standard formats and highlight some of the specific modifications made to the output metadata content to support the different conventions used by the multiple metadata integration endpoints.

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

PubMed

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.

A markup language for electrocardiogram data acquisition and analysis (ecgML)

PubMed Central

Wang, Haiying; Azuaje, Francisco; Jung, Benjamin; Black, Norman

2003-01-01

Background The storage and distribution of electrocardiogram data is based on different formats. There is a need to promote the development of standards for their exchange and analysis. Such models should be platform-/ system- and application-independent, flexible and open to every member of the scientific community. Methods A minimum set of information for the representation and storage of electrocardiogram signals has been synthesised from existing recommendations. This specification is encoded into an XML-vocabulary. The model may aid in a flexible exchange and analysis of electrocardiogram information. Results Based on advantages of XML technologies, ecgML has the ability to present a system-, application- and format-independent solution for representation and exchange of electrocardiogram data. The distinction between the proposal developed by the U.S Food and Drug Administration and ecgML model is given. A series of tools, which aim to facilitate ecgML-based applications, are presented. Conclusions The models proposed here can facilitate the generation of a data format, which opens ways for better and clearer interpretation by both humans and machines. Its structured and transparent organisation will allow researchers to expand and test its capabilities in different application domains. The specification and programs for this protocol are publicly available. PMID:12735790

Issues and solutions for storage, retrieval, and searching of MPEG-7 documents

NASA Astrophysics Data System (ADS)

Chang, Yuan-Chi; Lo, Ming-Ling; Smith, John R.

2000-10-01

The ongoing MPEG-7 standardization activity aims at creating a standard for describing multimedia content in order to facilitate the interpretation of the associated information content. Attempting to address a broad range of applications, MPEG-7 has defined a flexible framework consisting of Descriptors, Description Schemes, and Description Definition Language. Descriptors and Description Schemes describe features, structure and semantics of multimedia objects. They are written in the Description Definition Language (DDL). In the most recent revision, DDL applies XML (Extensible Markup Language) Schema with MPEG-7 extensions. DDL has constructs that support inclusion, inheritance, reference, enumeration, choice, sequence, and abstract type of Description Schemes and Descriptors. In order to enable multimedia systems to use MPEG-7, a number of important problems in storing, retrieving and searching MPEG-7 documents need to be solved. This paper reports on initial finding on issues and solutions of storing and accessing MPEG-7 documents. In particular, we discuss the benefits of using a virtual document management framework based on XML Access Server (XAS) in order to bridge the MPEG-7 multimedia applications and database systems. The need arises partly because MPEG-7 descriptions need customized storage schema, indexing and search engines. We also discuss issues arising in managing dependence and cross-description scheme search.

VOTable JAVA Streaming Writer and Applications.

NASA Astrophysics Data System (ADS)

Kulkarni, P.; Kembhavi, A.; Kale, S.

2004-07-01

Virtual Observatory related tools use a new standard for data transfer called the VOTable format. This is a variant of the xml format that enables easy transfer of data over the web. We describe a streaming interface that can bridge the VOTable format, through a user friendly graphical interface, with the FITS and ASCII formats, which are commonly used by astronomers. A streaming interface is important for efficient use of memory because of the large size of catalogues. The tools are developed in JAVA to provide a platform independent interface. We have also developed a stand-alone version that can be used to convert data stored in ASCII or FITS format on a local machine. The Streaming writer is successfully being used in VOPlot (See Kale et al 2004 for a description of VOPlot).We present the test results of converting huge FITS and ASCII data into the VOTable format on machines that have only limited memory.

MPEG-7: standard metadata for multimedia content

NASA Astrophysics Data System (ADS)

Chang, Wo

2005-08-01

The eXtensible Markup Language (XML) metadata technology of describing media contents has emerged as a dominant mode of making media searchable both for human and machine consumptions. To realize this premise, many online Web applications are pushing this concept to its fullest potential. However, a good metadata model does require a robust standardization effort so that the metadata content and its structure can reach its maximum usage between various applications. An effective media content description technology should also use standard metadata structures especially when dealing with various multimedia contents. A new metadata technology called MPEG-7 content description has merged from the ISO MPEG standards body with the charter of defining standard metadata to describe audiovisual content. This paper will give an overview of MPEG-7 technology and what impact it can bring forth to the next generation of multimedia indexing and retrieval applications.

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

PubMed

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.

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

PubMed Central

2010-01-01

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. PMID:21078179

Integration Framework of Process Planning based on Resource Independent Operation Summary to Support Collaborative Manufacturing

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

Kulvatunyou, Boonserm; Wysk, Richard A.; Cho, Hyunbo

2004-06-01

In today's global manufacturing environment, manufacturing functions are distributed as never before. Design, engineering, fabrication, and assembly of new products are done routinely in many different enterprises scattered around the world. Successful business transactions require the sharing of design and engineering data on an unprecedented scale. This paper describes a framework that facilitates the collaboration of engineering tasks, particularly process planning and analysis, to support such globalized manufacturing activities. The information models of data and the software components that integrate those information models are described. The integration framework uses an Integrated Product and Process Data (IPPD) representation called a Resourcemore » Independent Operation Summary (RIOS) to facilitate the communication of business and manufacturing requirements. Hierarchical process modeling, process planning decomposition and an augmented AND/OR directed graph are used in this representation. The Resource Specific Process Planning (RSPP) module assigns required equipment and tools, selects process parameters, and determines manufacturing costs based on two-level hierarchical RIOS data. The shop floor knowledge (resource and process knowledge) and a hybrid approach (heuristic and linear programming) to linearize the AND/OR graph provide the basis for the planning. Finally, a prototype system is developed and demonstrated with an exemplary part. Java and XML (Extensible Markup Language) are used to ensure software and information portability.« less

qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

PubMed Central

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

2014-01-01

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

PubMed

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

2014-08-01

Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Information object definition-based unified modeling language representation of DICOM structured reporting: a case study of transcoding DICOM to XML.

PubMed

Tirado-Ramos, Alfredo; Hu, Jingkun; Lee, K P

2002-01-01

Supplement 23 to DICOM (Digital Imaging and Communications for Medicine), Structured Reporting, is a specification that supports a semantically rich representation of image and waveform content, enabling experts to share image and related patient information. DICOM SR supports the representation of textual and coded data linked to images and waveforms. Nevertheless, the medical information technology community needs models that work as bridges between the DICOM relational model and open object-oriented technologies. The authors assert that representations of the DICOM Structured Reporting standard, using object-oriented modeling languages such as the Unified Modeling Language, can provide a high-level reference view of the semantically rich framework of DICOM and its complex structures. They have produced an object-oriented model to represent the DICOM SR standard and have derived XML-exchangeable representations of this model using World Wide Web Consortium specifications. They expect the model to benefit developers and system architects who are interested in developing applications that are compliant with the DICOM SR specification.

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.

PubMed

Wu, Gang; Zheng, Yuanpu; Qureshi, Imran; Zin, Htar Thant; Beck, Tyler; Bulka, Blazej; Freeland, Stephen J

2007-01-01

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.

XML-based scripting of multimodality image presentations in multidisciplinary clinical conferences

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Allada, Vivekanand; Dahlbom, Magdalena; Marcus, Phillip; Fine, Ian; Lapstra, Lorelle

2002-05-01

We developed a multi-modality image presentation software for display and analysis of images and related data from different imaging modalities. The software is part of a cardiac image review and presentation platform that supports integration of digital images and data from digital and analog media such as videotapes, analog x-ray films and 35 mm cine films. The software supports standard DICOM image files as well as AVI and PDF data formats. The system is integrated in a digital conferencing room that includes projections of digital and analog sources, remote videoconferencing capabilities, and an electronic whiteboard. The goal of this pilot project is to: 1) develop a new paradigm for image and data management for presentation in a clinically meaningful sequence adapted to case-specific scenarios, 2) design and implement a multi-modality review and conferencing workstation using component technology and customizable 'plug-in' architecture to support complex review and diagnostic tasks applicable to all cardiac imaging modalities and 3) develop an XML-based scripting model of image and data presentation for clinical review and decision making during routine clinical tasks and multidisciplinary clinical conferences.

Adapt

NASA Astrophysics Data System (ADS)

Bargatze, L. F.

2015-12-01

Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted files, or the addition of new or the deletion of old data products. Next, ADAPT routines analyzed the query results and issued updates to the metadata stored in the UCLA CDAWEB and SPDF metadata registries. In this way, the SPASE metadata registries generated by ADAPT can be relied on to provide up to date and complete access to Heliophysics CDF data resources on a daily basis.

Syntactic and Semantic Validation without a Metadata Management System

NASA Technical Reports Server (NTRS)

Pollack, Janine; Gokey, Christopher D.; Kendig, David; Olsen, Lola; Wharton, Stephen W. (Technical Monitor)

2001-01-01

The ability to maintain quality information is essential to securing the confidence in any system for which the information serves as a data source. NASA's Global Change Master Directory (GCMD), an online Earth science data locator, holds over 9000 data set descriptions and is in a constant state of flux as metadata are created and updated on a daily basis. In such a system, the importance of maintaining the consistency and integrity of these-metadata is crucial. The GCMD has developed a metadata management system utilizing XML, controlled vocabulary, and Java technologies to ensure the metadata not only adhere to valid syntax, but also exhibit proper semantics.

Comparison of Fingerprint and Iris Biometric Authentication for Control of Digital Signatures

PubMed Central

Zuckerman, Alan E.; Moon, Kenneth A.; Eaddy, Kenneth

2002-01-01

Biometric authentication systems can be used to control digital signature of medical documents. This pilot study evaluated the use of two different fingerprint technologies and one iris technology to control creation of digital signatures on a central server using public private key pairs stored on the server. Documents and signatures were stored in XML for portability. Key pairs and authentication certificates were generated during biometric enrollment. Usability and user acceptance were guarded and limitations of biometric systems prevented use of the system with all test subjects. The system detected alternations in the data content and provided future signer re-authentication for non-repudiation.

Digitising legacy zoological taxonomic literature: Processes, products and using the output

PubMed Central

Lyal, Christopher H. C.

2016-01-01

Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future. PMID:26877659

Implementing GermWatcher, an enterprise infection control application.

PubMed

Doherty, Joshua; Noirot, Laura A; Mayfield, Jennie; Ramiah, Sridhar; Huang, Christine; Dunagan, Wm Claiborne; Bailey, Thomas C

2006-01-01

Automated surveillance tools can provide significant advantages to infection control practitioners. When stored in a relational database, the data collected can also be used to support numerous research and quality improvement opportunities. A previously described electronic infection control surveillance system was remodeled to provide multi-hospital support, an XML based rule set, and interoperability with an enterprise terminology server. This paper describes the new architecture being used at hospitals across BJC HealthCare.

Solar Data | Geospatial Data Science | NREL

Science.gov Websites

System Name: WGS_1984 Coverage File Last Updated Metadata KMZ File Lower 48 and Hawaii DNI 10-km Resolution 1998-2009 Zip 9.6 MB 09/12/2012 Direct Normal.xml Direct Normal.kmz Lower 48 and Hawaii GHI 10-km : GCS_North_American_1983 Coverage File Last Updated Metadata KMZ File Lower 48 DNI 10-km Resolution 1998-2005 Zip 9.1 MB 12

PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

PubMed Central

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2006-01-01

Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

The NERC Vocabulary Server: Version 2.0

NASA Astrophysics Data System (ADS)

Leadbetter, A.; Lowry, R.; Clements, O.

2012-04-01

The NERC Vocabulary Server (NVS) has been used to publish controlled vocabularies of terms relevant to the marine environmental sciences domain since 2006 (version 0) with version 1 being introduced in 2007. It has been used for • metadata mark-up with verifiable content • populating dynamic drop down lists • semantic cross-walk between metadata schemata • so-called smart search • and the semantic enablement of Open Geospatial Consortium Web Processing Services in projects including: the NERC Data Grid; SeaDataNet; Geo-Seas; and the European Marine Observation and Data Network (EMODnet). The NVS is based on the Simple Knowledge Organization System (SKOS) model and following a version change for SKOS in 2009 there was a desire to upgrade the NVS to incorporate the changes in this standard. SKOS is based on the "concept", which it defines as a "unit of thought", that is an idea or notion such as "oil spill". The latest version of SKOS introduces the ability to aggregate concepts in both collections and schemes. The design of version 2 of the NVS uses both types of aggregation: schemes for the discovery of content through hierarchical thesauri and collections for the publication and addressing of content. Other desired changes from version 1 of the NVS included: • the removal of the potential for multiple Uniform Resource Names for the same concept to ensure consistent identification of concepts • the addition of content and technical governance information in the payload documents to provide an audit trail to users of NVS content • the removal of XML snippets from concept definitions in order to correctly validate XML serializations of the SKOS • the addition of the ability to map into external knowledge organization systems in order to extend the knowledge base • a more truly RESTful approach URL access to the NVS to make the development of applications on top of the NVS easier • and support for multiple human languages to increase the user base of the NVS Version 2 of the NVS underpins the semantic layer for the Open Service Network for Marine Environmental Data (NETMAR) project, funded by the European Commission under the Seventh Framework Programme. Here we present the results of upgrading the NVS from version 1 to 2 and show applications which have been built on top of the NVS using its Application Programming Interface, including a demonstration version of a SPARQL interface.

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Performance Comparison of Relational and Native-XML Databases using the Semantics of the Land Command and Control Information Exchange Data Model (LC2IEDM)

DTIC Science & Technology

2005-09-01

aid this thesis would not have come to existence. First, we would like to thank Eric Chaum for his enthusiasm and recommendation for doing this...by David Hina [HINA 00], discusses the use of available Commercial-Off-The-Shelf (COTS) XML technology to provide for the exchange of data between...air and maritime components and therefore forms the basis of a joint command and control data model [ CHAUM 04]. The data model is one of the two

CISN Display - Reliable Delivery of Real-time Earthquake Information, Including Rapid Notification and ShakeMap to Critical End Users

NASA Astrophysics Data System (ADS)

Rico, H.; Hauksson, E.; Thomas, E.; Friberg, P.; Given, D.

2002-12-01

The California Integrated Seismic Network (CISN) Display is part of a Web-enabled earthquake notification system alerting users in near real-time of seismicity, and also valuable geophysical information following a large earthquake. It will replace the Caltech/USGS Broadcast of Earthquakes (CUBE) and Rapid Earthquake Data Integration (REDI) Display as the principal means of delivering graphical earthquake information to users at emergency operations centers, and other organizations. Features distinguishing the CISN Display from other GUI tools are a state-full client/server relationship, a scalable message format supporting automated hyperlink creation, and a configurable platform-independent client with a GIS mapping tool; supporting the decision-making activities of critical users. The CISN Display is the front-end of a client/server architecture known as the QuakeWatch system. It is comprised of the CISN Display (and other potential clients), message queues, server, server "feeder" modules, and messaging middleware, schema and generators. It is written in Java, making it platform-independent, and offering the latest in Internet technologies. QuakeWatch's object-oriented design allows components to be easily upgraded through a well-defined set of application programming interfaces (APIs). Central to the CISN Display's role as a gateway to other earthquake products is its comprehensive XML-schema. The message model starts with the CUBE message format, but extends it by provisioning additional attributes for currently available products, and those yet to be considered. The supporting metadata in the XML-message provides the data necessary for the client to create a hyperlink and associate it with a unique event ID. Earthquake products deliverable to the CISN Display are ShakeMap, Ground Displacement, Focal Mechanisms, Rapid Notifications, OES Reports, and Earthquake Commentaries. Leveraging the power of the XML-format, the CISN Display provides prompt access to earthquake information on the Web. The links are automatically created when product generators deliver CUBE formatted packets to a Quake Data Distribution System (QDDS) hub (new distribution methods may be used later). The "feeder" modules tap into the QDDS hub and convert the packets into XML-messages. These messages are forwarded to message queues, and then distributed to clients where URLs are dynamically created for these products and linked to events on the CISN Display map. The products may be downloaded out-of-band; and with the inclusion of a GIS mapping tool users can plot organizational assets on the CISN Display map and overlay them against key spectral data, such as ground accelerations. This gives Emergency Response Managers information useful in allocating limited personnel and resources after a major event. At the heart of the system's robustness is a well-established and reliable set of communication protocols for best-effort delivery of data. For critical users a Common Object Request Broker Architecture (CORBA) state-full connection is used via a dedicated signaling channel. The system employs several CORBA methods that alert users of changes in the link status. Loss of connectivity triggers a strategy that attempts to reconnect through various physical and logical paths. Thus, by building on past application successes and proven Internet advances the CISN Display targets a specific audience by providing enhancements previously not available from other applications.

A Framework to Manage Information Models

NASA Astrophysics Data System (ADS)

Hughes, J. S.; King, T.; Crichton, D.; Walker, R.; Roberts, A.; Thieman, J.

2008-05-01

The Information Model is the foundation on which an Information System is built. It defines the entities to be processed, their attributes, and the relationships that add meaning. The development and subsequent management of the Information Model is the single most significant factor for the development of a successful information system. A framework of tools has been developed that supports the management of an information model with the rigor typically afforded to software development. This framework provides for evolutionary and collaborative development independent of system implementation choices. Once captured, the modeling information can be exported to common languages for the generation of documentation, application databases, and software code that supports both traditional and semantic web applications. This framework is being successfully used for several science information modeling projects including those for the Planetary Data System (PDS), the International Planetary Data Alliance (IPDA), the National Cancer Institute's Early Detection Research Network (EDRN), and several Consultative Committee for Space Data Systems (CCSDS) projects. The objective of the Space Physics Archive Search and Exchange (SPASE) program is to promote collaboration and coordination of archiving activity for the Space Plasma Physics community and ensure the compatibility of the architectures used for a global distributed system and the individual data centers. Over the past several years, the SPASE data model working group has made great progress in developing the SPASE Data Model and supporting artifacts including a data dictionary, XML Schema, and two ontologies. The authors have captured the SPASE Information Model in this framework. This allows the generation of documentation that presents the SPASE Information Model in object-oriented notation including UML class diagrams and class hierarchies. The modeling information can also be exported to semantic web languages such as OWL and RDF and written to XML Metadata Interchange (XMI) files for import into UML tools.

Development Of International Data Standards For The COSMOS/PEER-LL Virtual Data Center

NASA Astrophysics Data System (ADS)

Swift, J. N.

2005-12-01

The COSMOS -PEER Lifelines Project 2L02 completed a Pilot Geotechnical Virtual Data Center (GVDC) system capable of both archiving geotechnical data and of disseminating data from multiple linked geotechnical databases. The Pilot GVDC system links geotechnical databases of four organizations: the California Geological Survey, Caltrans, PG&E, and the U. S. Geological Survey The System was presented and reviewed in the COSMOS-PEER Lifelines workshop on June 21 - 23, 2004, which was co-sponsored by the Federal Highway Administration (FHWA) and included participation by the United Kingdom Highways Agency (UKHA) , the Association of Geotechnical and Geoenvironmental Specialists in the United Kingdom (AGS), the United States Army Corp of Engineers (USACOE), Caltrans, United States Geological Survey (USGS), California Geological Survey (CGS), a number of state Departments of Transportation (DOTs), county building code officials, and representatives of academic institutions and private sector geotechnical companies. As of February 2005 COSMOS-PEER Lifelines Project 2L03 is currently funded to accomplish the following tasks: 1) expand the Pilot GVDC Geotechnical Data Dictionary and XML Schema to include data definitions and structures to describe in-situ measurements such as shear wave velocity profiles, and additional laboratory geotechnical test types; 2) participate in an international cooperative working group developing a single geotechnical data exchange standard that has broad international acceptance; and 3) upgrade the GVDC system to support corresponding exchange standard data dictionary and schema improvements. The new geophysical data structures being developed will include PS-logs, downhole geophysical logs, cross-hole velocity data, and velocity profiles derived using surface waves. A COSMOS-PEER Lifelines Geophysical Data Dictionary Working Committee constituted of experts in the development of data dictionary standards and experts in the specific data to be captured are presently working on this task. The international geotechnical data dictionary and schema development is a highly collaborative effort funded by a pooled fund study coordinated by state DOTs and FHWA. The technical development of the standards called DIGGS (Data Interchange for Geotechnical and Geoenvironmental Specialists) is lead by a team consisting of representatives from the University of Florida, Department of Civil Engineering (UF), AGS, Construction Industry Research and Information Association (CIRIA), UKHA, Ohio DOT, and COSMOS. The first draft of DIGGS is currently in preparation. A Geotechnical Management System Group (GMS group), composed of representatives from 13 State DOTs, FHWA, US EPA, USACOE, USGS and UKHA, oversees and approves the development of the standards. The ultimate goal of both COSMOS-PEER Lifelines Project 2L03 and the international GMS working group is to produce open and flexible, GML-compliant XML schema-based data structures and data dictionaries for review and approval by DOTs, other public agencies, and the international engineering and geoenvironmental community at large, leading to adoption of internationally accepted geotechnical and geophysical data transfer standards. Establishment of these standards is intended to significantly facilitate the accessibility and exchange of geotechnical information world wide.

Achieving mask order processing automation, interoperability and standardization based on P10

NASA Astrophysics Data System (ADS)

Rodriguez, B.; Filies, O.; Sadran, D.; Tissier, Michel; Albin, D.; Stavroulakis, S.; Voyiatzis, E.

2007-02-01

Last year the MUSCLE (Masks through User's Supply Chain: Leadership by Excellence) project was presented. Here is the project advancement. A key process in mask supply chain management is the exchange of technical information for ordering masks. This process is large, complex, company specific and error prone, and leads to longer cycle times and higher costs due to missing or wrong inputs. Its automation and standardization could produce significant benefits. We need to agree on the standard for mandatory and optional parameters, and also a common way to describe parameters when ordering. A system was created to improve the performance in terms of Key Performance Indicators (KPIs) such as cycle time and cost of production. This tool allows us to evaluate and measure the effect of factors, as well as the effect of implementing the improvements of the complete project. Next, a benchmark study and a gap analysis were performed. These studies show the feasibility of standardization, as there is a large overlap in requirements. We see that the SEMI P10 standard needs enhancements. A format supporting the standard is required, and XML offers the ability to describe P10 in a flexible way. Beyond using XML for P10, the semantics of the mask order should also be addressed. A system design and requirements for a reference implementation for a P10 based management system are presented, covering a mechanism for the evolution and for version management and a design for P10 editing and data validation.

Enabling private and public sector organizations as agents of homeland security

NASA Astrophysics Data System (ADS)

Glassco, David H. J.; Glassco, Jordan C.

2006-05-01

Homeland security and defense applications seek to reduce the risk of undesirable eventualities across physical space in real-time. With that functional requirement in mind, our work focused on the development of IP based agent telecommunication solutions for heterogeneous sensor / robotic intelligent "Things" that could be deployed across the internet. This paper explains how multi-organization information and device sharing alliances may be formed to enable organizations to act as agents of homeland security (in addition to other uses). Topics include: (i) using location-aware, agent based, real-time information sharing systems to integrate business systems, mobile devices, sensor and actuator based devices and embedded devices used in physical infrastructure assets, equipment and other man-made "Things"; (ii) organization-centric real-time information sharing spaces using on-demand XML schema formatted networks; (iii) object-oriented XML serialization as a methodology for heterogeneous device glue code; (iv) how complex requirements for inter / intra organization information and device ownership and sharing, security and access control, mobility and remote communication service, tailored solution life cycle management, service QoS, service and geographic scalability and the projection of remote physical presence (through sensing and robotics) and remote informational presence (knowledge of what is going elsewhere) can be more easily supported through feature inheritance with a rapid agent system development methodology; (v) how remote object identification and tracking can be supported across large areas; (vi) how agent synergy may be leveraged with analytics to complement heterogeneous device networks.

Towards the Development of a Unified Distributed Date System for L1 Spacecraft

NASA Technical Reports Server (NTRS)

Lazarus, Alan J.; Kasper, Justin C.

2005-01-01

The purpose of this grant, 'Towards the Development of a Unified Distributed Data System for L1 Spacecraft', is to take the initial steps towards the development of a data distribution mechanism for making in-situ measurements more easily accessible to the scientific community. Our obligations as subcontractors to this grant are to add our Faraday Cup plasma data to this initial study and to contribute to the design of a general data distribution system. The year 1 objectives of the overall project as stated in the GSFC proposal are: 1) Both the rsync and Perl based data exchange tools will be fully developed and tested in our mixed, Unix, VMS, Windows and Mac OS X data service environment. Based on the performance comparisons, one will be selected and fully deployed. Continuous data exchange between all L1 solar wind monitors initiated. 2) Data version metadata will be agreed upon, fully documented, and deployed on our data sites. 3) The first version of the data description rules, encoded in a XML Schema, will be finalized. 4) Preliminary set of library routines will be collected, documentation standards and formats agreed on, and desirable routines that have not been implemented identified and assigned. 5) ViSBARD test site implemented to independently validate data mirroring procedures. The specific MIT tasks over the duration of this project are the following: a) implement mirroring service for WIND plasma data b) participate in XML Schema development c) contribute toward routine library.

A Services-Oriented Architecture for Water Observations Data

NASA Astrophysics Data System (ADS)

Maidment, D. R.; Zaslavsky, I.; Valentine, D.; Tarboton, D. G.; Whitenack, T.; Whiteaker, T.; Hooper, R.; Kirschtel, D.

2009-04-01

Water observations data are time series of measurements made at point locations of water level, flow, and quality and corresponding data for climatic observations at point locations such as gaged precipitation and weather variables. A services-oriented architecture has been built for such information for the United States that has three components: hydrologic information servers, hydrologic information clients, and a centralized metadata cataloging system. These are connected using web services for observations data and metadata defined by an XML-based language called WaterML. A Hydrologic Information Server can be built by storing observations data in a relational database schema in the CUAHSI Observations Data Model, in which case, web services access to the data and metadata is automatically provided by query functions for WaterML that are wrapped around the relational database within a web server. A Hydrologic Information Server can also be constructed by custom-programming an interface to an existing water agency web site so that responds to the same queries by producing data in WaterML as do the CUAHSI Observations Data Model based servers. A Hydrologic Information Client is one which can interpret and ingest WaterML metadata and data. We have two client applications for Excel and ArcGIS and have shown how WaterML web services can be ingested into programming environments such as Matlab and Visual Basic. HIS Central, maintained at the San Diego Supercomputer Center is a repository of observational metadata for WaterML web services which presently indexes 342 million data measured at 1.75 million locations. This is the largest catalog water observational data for the United States presently in existence. As more observation networks join what we term "CUAHSI Water Data Federation", and the system accommodates a growing number of sites, measured parameters, applications, and users, rapid and reliable access to large heterogeneous hydrologic data repositories becomes critical. The CUAHSI HIS solution to the scalability and heterogeneity challenges has several components. Structural differences across the data repositories are addressed by building a standard services foundation for the exchange of hydrologic data, as derived from a common information model for observational data measured at stationary points and its implementation as a relational schema (ODM) and an XML schema (WaterML). Semantic heterogeneity is managed by mapping water quantity, water quality, and other parameters collected by government agencies and academic projects to a common ontology. The WaterML-compliant web services are indexed in a community services registry called HIS Central (hiscentral.cuahsi.org). Once a web service is registered in HIS Central, its metadata (site and variable characteristics, period of record for each variable at each site, etc.) is harvested and appended to the central catalog. The catalog is further updated as the service publisher associates the variables in the published service with ontology concepts. After this, the newly published service becomes available for spatial and semantics-based queries from online and desktop client applications developed by the project. Hydrologic system server software is now deployed at more than a dozen locations in the United States and Australia. To provide rapid access to data summaries, in particular for several nation-wide data repositories including EPA STORET, USGS NWIS, and USDA SNOTEL, we convert the observation data catalogs and databases with harvested data values into special representations that support high-performance analysis and visualization. The construction of OLAP (Online Analytical Processing) cubes, often called data cubes, is an approach to organizing and querying large multi-dimensional data collections. We have applied the OLAP techniques, as implemented in Microsoft SQL Server 2005/2008, to the analysis of the catalogs from several agencies. OLAP analysis results reflect geography and history of observation data availability from USGS NWIS, EPA STORET, and USDA SNOTEL repositories, and spatial and temporal dynamics of the available measurements for several key nutrient-related parameters. Our experience developing the CUAHSI HIS cyberinfrastructure demonstrated that efficient integration of hydrologic observations from multiple government and academic sources requires a range of technical approaches focused on managing different components of data heterogeneity and system scalability. While this submission addresses technical aspects of developing a national-scale information system for hydrologic observations, the challenges of explicating shared semantics of hydrologic observations and building a community of HIS users and developers remain critical in constructing a nation-wide federation of water data services.

Intelligent Visualization of Geo-Information on the Future Web

NASA Astrophysics Data System (ADS)

Slusallek, P.; Jochem, R.; Sons, K.; Hoffmann, H.

2012-04-01

Visualization is a key component of the "Observation Web" and will become even more important in the future as geo data becomes more widely accessible. The common statement that "Data that cannot be seen, does not exist" is especially true for non-experts, like most citizens. The Web provides the most interesting platform for making data easily and widely available. However, today's Web is not well suited for the interactive visualization and exploration that is often needed for geo data. Support for 3D data was added only recently and at an extremely low level (WebGL), but even the 2D visualization capabilities of HTML e.g. (images, canvas, SVG) are rather limited, especially regarding interactivity. We have developed XML3D as an extension to HTML-5. It allows for compactly describing 2D and 3D data directly as elements of an HTML-5 document. All graphics elements are part of the Document Object Model (DOM) and can be manipulated via the same set of DOM events and methods that millions of Web developers use on a daily basis. Thus, XML3D makes highly interactive 2D and 3D visualization easily usable, not only for geo data. XML3D is supported by any WebGL-capable browser but we also provide native implementations in Firefox and Chromium. As an example, we show how OpenStreetMap data can be mapped directly to XML3D and visualized interactively in any Web page. We show how this data can be easily augmented with additional data from the Web via a few lines of Javascript. We also show how embedded semantic data (via RDFa) allows for linking the visualization back to the data's origin, thus providing an immersive interface for interacting with and modifying the original data. XML3D is used as key input for standardization within the W3C Community Group on "Declarative 3D for the Web" chaired by the DFKI and has recently been selected as one of the Generic Enabler for the EU Future Internet initiative.

Information persistence using XML database technology

NASA Astrophysics Data System (ADS)

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 improved retrieval techniques.

SU-F-P-36: Automation of Linear Accelerator Star Shot Measurement with Advanced XML Scripting and Electronic Portal Imaging Device

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

Nguyen, N; Knutson, N; Schmidt, M

Purpose: To verify a method used to automatically acquire jaw, MLC, collimator and couch star shots for a Varian TrueBeam linear accelerator utilizing Developer Mode and an Electronic Portal Imaging Device (EPID). Methods: An XML script was written to automate motion of the jaws, MLC, collimator and couch in TrueBeam Developer Mode (TBDM) to acquire star shot measurements. The XML script also dictates MV imaging parameters to facilitate automatic acquisition and recording of integrated EPID images. Since couch star shot measurements cannot be acquired using a combination of EPID and jaw/MLC collimation alone due to a fixed imager geometry, amore » method utilizing a 5mm wide steel ruler placed on the table and centered within a 15×15cm2 open field to produce a surrogate of the narrow field aperture was investigated. Four individual star shot measurements (X jaw, Y jaw, MLC and couch) were obtained using our proposed as well as traditional film-based method. Integrated EPID images and scanned measurement films were analyzed and compared. Results: Star shot (X jaw, Y jaw, MLC and couch) measurements were obtained in a single 5 minute delivery using the TBDM XML script method compared to 60 minutes for equivalent traditional film measurements. Analysis of the images and films demonstrated comparable isocentricity results, agreeing within 0.3mm of each other. Conclusion: The presented automatic approach of acquiring star shot measurements using TBDM and EPID has proven to be more efficient than the traditional film approach with equivalent results.« less

Poster — Thur Eve — 55: An automated XML technique for isocentre verification on the Varian TrueBeam

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

Asiev, Krum; Mullins, Joel; DeBlois, François

2014-08-15

Isocentre verification tests, such as the Winston-Lutz (WL) test, have gained popularity in the recent years as techniques such as stereotactic radiosurgery/radiotherapy (SRS/SRT) treatments are more commonly performed on radiotherapy linacs. These highly conformal treatments require frequent monitoring of the geometrical accuracy of the isocentre to ensure proper radiation delivery. At our clinic, the WL test is performed by acquiring with the EPID a collection of 8 images of a WL phantom fixed on the couch for various couch/gantry angles. This set of images is later analyzed to determine the isocentre size. The current work addresses the acquisition process. Amore » manual WL test acquisition performed by and experienced physicist takes in average 25 minutes and is prone to user manipulation errors. We have automated this acquisition on a Varian TrueBeam STx linac (Varian, Palo Alto, USA). The Varian developer mode allows the execution of custom-made XML script files to control all aspects of the linac operation. We have created an XML-WL script that cycles through each couch/gantry combinations taking an EPID image at each position. This automated acquisition is done in less than 4 minutes. The reproducibility of the method was verified by repeating the execution of the XML file 5 times. The analysis of the images showed variation of the isocenter size less than 0.1 mm along the X, Y and Z axes and compares favorably to a manual acquisition for which we typically observe variations up to 0.5 mm.« less

Lapin Data Interchange Among Database, Analysis and Display Programs Using XML-Based Text Files

NASA Technical Reports Server (NTRS)

2005-01-01

The purpose of grant NCC3-966 was to investigate and evaluate the interchange of application-specific data among multiple programs each carrying out part of the analysis and design task. This has been carried out previously by creating a custom program to read data produced by one application and then write that data to a file whose format is specific to the second application that needs all or part of that data. In this investigation, data of interest is described using the XML markup language that allows the data to be stored in a text-string. Software to transform output data of a task into an XML-string and software to read an XML string and extract all or a portion of the data needed for another application is used to link two independent applications together as part of an overall design effort. This approach was initially used with a standard analysis program, Lapin, along with standard applications a standard spreadsheet program, a relational database program, and a conventional dialog and display program to demonstrate the successful sharing of data among independent programs. Most of the effort beyond that demonstration has been concentrated on the inclusion of more complex display programs. Specifically, a custom-written windowing program organized around dialogs to control the interactions have been combined with an independent CAD program (Open Cascade) that supports sophisticated display of CAD elements such as lines, spline curves, and surfaces and turbine-blade data produced by an independent blade design program (UD0300).

NASA Tech Briefs, December 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics covered include: Video Mosaicking for Inspection of Gas Pipelines; Shuttle-Data-Tape XML Translator; Highly Reliable, High-Speed, Unidirectional Serial Data Links; Data-Analysis System for Entry, Descent, and Landing; Hybrid UV Imager Containing Face-Up AlGaN/GaN Photodiodes; Multiple Embedded Processors for Fault-Tolerant Computing; Hybrid Power Management; Magnetometer Based on Optoelectronic Microwave Oscillator; Program Predicts Time Courses of Human/ Computer Interactions; Chimera Grid Tools; Astronomer's Proposal Tool; Conservative Patch Algorithm and Mesh Sequencing for PAB3D; Fitting Nonlinear Curves by Use of Optimization Techniques; Tool for Viewing Faults Under Terrain; Automated Synthesis of Long Communication Delays for Testing; Solving Nonlinear Euler Equations With Arbitrary Accuracy; Self-Organizing-Map Program for Analyzing Multivariate Data; Tool for Sizing Analysis of the Advanced Life Support System; Control Software for a High-Performance Telerobot; Java Radar Analysis Tool; Architecture for Verifiable Software; Tool for Ranking Research Options; Enhanced, Partially Redundant Emergency Notification System; Close-Call Action Log Form; Task Description Language; Improved Small-Particle Powders for Plasma Spraying; Bonding-Compatible Corrosion Inhibitor for Rinsing Metals; Wipes, Coatings, and Patches for Detecting Hydrazines; Rotating Vessels for Growing Protein Crystals; Oscillating-Linear-Drive Vacuum Compressor for CO2; Mechanically Biased, Hinged Pairs of Piezoelectric Benders; Apparatus for Precise Indium-Bump Bonding of Microchips; Radiation Dosimetry via Automated Fluorescence Microscopy; Multistage Magnetic Separator of Cells and Proteins; Elastic-Tether Suits for Artificial Gravity and Exercise; Multichannel Brain-Signal-Amplifying and Digitizing System; Ester-Based Electrolytes for Low-Temperature Li-Ion Cells; Hygrometer for Detecting Water in Partially Enclosed Volumes; Radio-Frequency Plasma Cleaning of a Penning Malmberg Trap; Reduction of Flap Side Edge Noise - the Blowing Flap; and Preventing Accidental Ignition of Upper-Stage Rocket Motors.

Personalising e-learning modules: targeting Rasmussen levels using XML.

PubMed

Renard, J M; Leroy, S; Camus, H; Picavet, M; Beuscart, R

2003-01-01

The development of Internet technologies has made it possible to increase the number and the diversity of on-line resources for teachers and students. Initiatives like the French-speaking Virtual Medical University Project (UMVF) try to organise the access to these resources. But both teachers and students are working on a partly redundant subset of knowledge. From the analysis of some French courses we propose a model for knowledge organisation derived from Rasmussen's stepladder. In the context of decision-making Rasmussen has identified skill-based, rule-based and knowledge-based levels for the mental process. In the medical context of problem-solving, we apply these three levels to the definition of three students levels: beginners, intermediate-level learners, experts. Based on our model, we build a representation of the hierarchical structure of data using XML language. We use XSLT Transformation Language in order to filter relevant data according to student level and to propose an appropriate display on students' terminal. The model and the XML implementation we define help to design tools for building personalised e-learning modules.

Content-Aware DataGuide with Incremental Index Update using Frequently Used Paths

NASA Astrophysics Data System (ADS)

Sharma, A. K.; Duhan, Neelam; Khattar, Priyanka

2010-11-01

Size of the WWW is increasing day by day. Due to the absence of structured data on the Web, it becomes very difficult for information retrieval tools to fully utilize the Web information. As a solution to this problem, XML pages come into play, which provide structural information to the users to some extent. Without efficient indexes, query processing can be quite inefficient due to an exhaustive traversal on XML data. In this paper an improved content-centric approach of Content-Aware DataGuide, which is an indexing technique for XML databases, is being proposed that uses frequently used paths from historical query logs to improve query performance. The index can be updated incrementally according to the changes in query workload and thus, the overhead of reconstruction can be minimized. Frequently used paths are extracted using any Sequential Pattern mining algorithm on subsequent queries in the query workload. After this, the data structures are incrementally updated. This indexing technique proves to be efficient as partial matching queries can be executed efficiently and users can now get the more relevant documents in results.

An XML-based interchange format for genotype-phenotype data.

PubMed

Whirl-Carrillo, M; Woon, M; Thorn, C F; Klein, T E; Altman, R B

2008-02-01

Recent advances in high-throughput genotyping and phenotyping have accelerated the creation of pharmacogenomic data. Consequently, the community requires standard formats to exchange large amounts of diverse information. To facilitate the transfer of pharmacogenomics data between databases and analysis packages, we have created a standard XML (eXtensible Markup Language) schema that describes both genotype and phenotype data as well as associated metadata. The schema accommodates information regarding genes, drugs, diseases, experimental methods, genomic/RNA/protein sequences, subjects, subject groups, and literature. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB; www.pharmgkb.org) has used this XML schema for more than 5 years to accept and process submissions containing more than 1,814,139 SNPs on 20,797 subjects using 8,975 assays. Although developed in the context of pharmacogenomics, the schema is of general utility for exchange of genotype and phenotype data. We have written syntactic and semantic validators to check documents using this format. The schema and code for validation is available to the community at http://www.pharmgkb.org/schema/index.html (last accessed: 8 October 2007). (c) 2007 Wiley-Liss, Inc.

The XML Metadata Editor of GFZ Data Services

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Elger, Kirsten; Tesei, Telemaco; Trippanera, Daniele

2017-04-01

Following the FAIR data principles, research data should be Findable, Accessible, Interoperable and Reuseable. Publishing data under these principles requires to assign persistent identifiers to the data and to generate rich machine-actionable metadata. To increase the interoperability, metadata should include shared vocabularies and crosslink the newly published (meta)data and related material. However, structured metadata formats tend to be complex and are not intended to be generated by individual scientists. Software solutions are needed that support scientists in providing metadata describing their data. To facilitate data publication activities of 'GFZ Data Services', we programmed an XML metadata editor that assists scientists to create metadata in different schemata popular in the earth sciences (ISO19115, DIF, DataCite), while being at the same time usable by and understandable for scientists. Emphasis is placed on removing barriers, in particular the editor is publicly available on the internet without registration [1] and the scientists are not requested to provide information that may be generated automatically (e.g. the URL of a specific licence or the contact information of the metadata distributor). Metadata are stored in browser cookies and a copy can be saved to the local hard disk. To improve usability, form fields are translated into the scientific language, e.g. 'creators' of the DataCite schema are called 'authors'. To assist filling in the form, we make use of drop down menus for small vocabulary lists and offer a search facility for large thesauri. Explanations to form fields and definitions of vocabulary terms are provided in pop-up windows and a full documentation is available for download via the help menu. In addition, multiple geospatial references can be entered via an interactive mapping tool, which helps to minimize problems with different conventions to provide latitudes and longitudes. Currently, we are extending the metadata editor to be reused to generate metadata for data discovery and contextual metadata developed by the 'Multi-scale Laboratories' Thematic Core Service of the European Plate Observing System (EPOS-IP). The Editor will be used to build a common repository of a large variety of geological and geophysical datasets produced by multidisciplinary laboratories throughout Europe, thus contributing to a significant step toward the integration and accessibility of earth science data. This presentation will introduce the metadata editor and show the adjustments made for EPOS-IP. [1] http://dataservices.gfz-potsdam.de/panmetaworks/metaedit

ALMA software architecture

NASA Astrophysics Data System (ADS)

Schwarz, Joseph; Raffi, Gianni

2002-12-01

The Atacama Large Millimeter Array (ALMA) is a joint project involving astronomical organizations in Europe and North America. ALMA will consist of at least 64 12-meter antennas operating in the millimeter and sub-millimeter range. It will be located at an altitude of about 5000m in the Chilean Atacama desert. The primary challenge to the development of the software architecture is the fact that both its development and runtime environments will be distributed. Groups at different institutes will develop the key elements such as Proposal Preparation tools, Instrument operation, On-line calibration and reduction, and Archiving. The Proposal Preparation software will be used primarily at scientists' home institutions (or on their laptops), while Instrument Operations will execute on a set of networked computers at the ALMA Operations Support Facility. The ALMA Science Archive, itself to be replicated at several sites, will serve astronomers worldwide. Building upon the existing ALMA Common Software (ACS), the system architects will prepare a robust framework that will use XML-encoded entity objects to provide an effective solution to the persistence needs of this system, while remaining largely independent of any underlying DBMS technology. Independence of distributed subsystems will be facilitated by an XML- and CORBA-based pass-by-value mechanism for exchange of objects. Proof of concept (as well as a guide to subsystem developers) will come from a prototype whose details will be presented.

Creating XML/PHP Interface for BAN Interoperability.

PubMed

Fragkos, Vasileios; Katzis, Konstantinos; Despotou, Georgios

2017-01-01

Recent advances in medical and electronic technologies have introduced the use of Body Area Networks as a part of e-health, for constant and accurate monitoring of patients and the transmission as well as processing of the data to develop a holistic Electronic Health Record. The rising global population, different BAN manufacturers and a variety of medical systems pose the issue of interoperability between BANs and systems as well as the proper way to propagate medical data in an organized and efficient manner. In this paper, we describe BANs and propose the use of certain web technologies to address this issue.