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.

78 FR 25749 - Submission of New Drug Application/Abbreviated New Drug Application Field Alert Reports: Notice...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-02

... language)-enabled Adobe PDF form, Form FDA 3331--Automated to submit new drug application (NDA) and...-enabled Adobe PDF form, Form FDA 3331--Automated, will be available for piloting between May 1, 2013, and... modernize the FAR submission and review pathway using an XML-enabled PDF form to enable integration with...

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

Kim, Joyce Jihyun; Yin, Rongxin; Kiliccote, Sila

Open Automated Demand Response (OpenADR), an XML-based information exchange model, is used to facilitate continuous price-responsive operation and demand response participation for large commercial buildings in New York who are subject to the default day-ahead hourly pricing. We summarize the existing demand response programs in New York and discuss OpenADR communication, prioritization of demand response signals, and control methods. Building energy simulation models are developed and field tests are conducted to evaluate continuous energy management and demand response capabilities of two commercial buildings in New York City. Preliminary results reveal that providing machine-readable prices to commercial buildings can facilitate bothmore » demand response participation and continuous energy cost savings. Hence, efforts should be made to develop more sophisticated algorithms for building control systems to minimize customer's utility bill based on price and reliability information from the electricity grid.« less

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.

A semi-automated tool for treatment plan-quality evaluation and clinical trial quality assurance

NASA Astrophysics Data System (ADS)

Wang, Jiazhou; Chen, Wenzhou; Studenski, Matthew; Cui, Yunfeng; Lee, Andrew J.; Xiao, Ying

2013-07-01

The goal of this work is to develop a plan-quality evaluation program for clinical routine and multi-institutional clinical trials so that the overall evaluation efficiency is improved. In multi-institutional clinical trials evaluating the plan quality is a time-consuming and labor-intensive process. In this note, we present a semi-automated plan-quality evaluation program which combines MIMVista, Java/MATLAB, and extensible markup language (XML). More specifically, MIMVista is used for data visualization; Java and its powerful function library are implemented for calculating dosimetry parameters; and to improve the clarity of the index definitions, XML is applied. The accuracy and the efficiency of the program were evaluated by comparing the results of the program with the manually recorded results in two RTOG trials. A slight difference of about 0.2% in volume or 0.6 Gy in dose between the semi-automated program and manual recording was observed. According to the criteria of indices, there are minimal differences between the two methods. The evaluation time is reduced from 10-20 min to 2 min by applying the semi-automated plan-quality evaluation program.

Production Maintenance Infrastructure

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

Jason Gabler, David Skinner

2005-11-01

PMI is a XML framework for formulating tests of software and software environments which operate in a relatively push button manner, i.e., can be automated, and that provide results that are readily consumable/publishable via RSS. Insofar as possible the tests are carried out in manner congruent with real usage. PMI drives shell scripts via a perl program which is charge of timing, validating each test, and controlling the flow through sets of tests. Testing in PMI is built up hierarchically. A suite of tests may start by testing basic functionalities (file system is writable, compiler is found and functions, shellmore » environment behaves as expected, etc.) and work up to large more complicated activities (execution of parallel code, file transfers, etc.) At each step in this hierarchy a failure leads to generation of a text message or RSS that can be tagged as to who should be notified of the failure. There are two functionalities that PMI has been directed at. 1) regular and automated testing of multi user environments and 2) version-wise testing of new software releases prior to their deployment in a production mode.« less

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.

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.

Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators.

PubMed

Murray-Rust, Peter; Rzepa, Henry S; Williamson, Mark J; Willighagen, Egon L

2004-01-01

Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.

Development strategies for the satellite flight software on-board Meteosat Third Generation

NASA Astrophysics Data System (ADS)

Tipaldi, Massimo; Legendre, Cedric; Koopmann, Olliver; Ferraguto, Massimo; Wenker, Ralf; D'Angelo, Gianni

2018-04-01

Nowadays, satellites are becoming increasingly software dependent. Satellite Flight Software (FSW), that is to say, the application software running on the satellite main On-Board Computer (OBC), plays a relevant role in implementing complex space mission requirements. In this paper, we examine relevant technical approaches and programmatic strategies adopted for the development of the Meteosat Third Generation Satellite (MTG) FSW. To begin with, we present its layered model-based architecture, and the means for ensuring a robust and reliable interaction among the FSW components. Then, we focus on the selection of an effective software development life cycle model. In particular, by combining plan-driven and agile approaches, we can fulfill the need of having preliminary SW versions. They can be used for the elicitation of complex system-level requirements as well as for the initial satellite integration and testing activities. Another important aspect can be identified in the testing activities. Indeed, very demanding quality requirements have to be fulfilled in satellite SW applications. This manuscript proposes a test automation framework, which uses an XML-based test procedure language independent of the underlying test environment. Finally, a short overview of the MTG FSW sizing and timing budgets concludes the paper.

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

Semantically Interoperable XML Data

PubMed Central

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

2013-01-01

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

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

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.

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.

Minimum information required for a DMET experiment reporting.

PubMed

Kumuthini, Judit; Mbiyavanga, Mamana; Chimusa, Emile R; Pathak, Jyotishman; Somervuo, Panu; Van Schaik, Ron Hn; Dolzan, Vita; Mizzi, Clint; Kalideen, Kusha; Ramesar, Raj S; Macek, Milan; Patrinos, George P; Squassina, Alessio

2016-09-01

To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases. For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting. MIDE provides reporting guidelines and describes the information required for reporting, data storage and data sharing in the form of XML. The MIDE guidelines will benefit the scientific community with pharmacogenomics experiments, including reporting pharmacogenomics data from other technology platforms, with the tools that will ease and automate the generation of such reports using the standardized MIDE XML schema, facilitating the sharing, dissemination, reanalysis of datasets through accessible and transparent pharmacogenomics data reporting.

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.

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 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.

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.

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.

User-Centered Authentication: LDAP, WRAP, X.509, XML (SIG LAN: Library Automation and Networks).

ERIC Educational Resources Information Center

Coble, Jim

2000-01-01

Presents an abstract for a planned panel session on technologies for user-centered authentication and authorization currently deployed in pilot or production implementations in academic computing. Presentations included: "Implementing LSAP for Single-Password Access to Campus Resources" (Layne Nordgren); "Implementing a Scalable…

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

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.

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.

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.

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.

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…

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.

Cloud parallel processing of tandem mass spectrometry based proteomics data.

PubMed

Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

2012-10-05

Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

Microprocessor-controlled, wide-range streak camera

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

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

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/

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.

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.

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.

On Logic and Standards for Structuring Documents

NASA Astrophysics Data System (ADS)

Eyers, David M.; Jones, Andrew J. I.; Kimbrough, Steven O.

The advent of XML has been widely seized upon as an opportunity to develop document representation standards that lend themselves to automated processing. This is a welcome development and much good has come of it. That said, present standardization efforts may be criticized on a number of counts. We explore two issues associated with document XML standardization efforts. We label them (i) the dynamic point and (ii) the logical point. Our dynamic point is that in many cases experience has shown that the search for a final, or even reasonably permanent, document representation standard is futile. The case is especially strong for electronic data interchange (EDI). Our logical point is that formalization into symbolic logic is materially helpful for understanding and designing dynamic document standards.

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.

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.

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.

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.

XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

PubMed

Ahmed, Wamiq M; Lenz, Dominik; Liu, Jia; Paul Robinson, J; Ghafoor, Arif

2008-03-01

High-throughput biological imaging uses automated imaging devices to collect a large number of microscopic images for analysis of biological systems and validation of scientific hypotheses. Efficient manipulation of these datasets for knowledge discovery requires high-performance computational resources, efficient storage, and automated tools for extracting and sharing such knowledge among different research sites. Newly emerging grid technologies provide powerful means for exploiting the full potential of these imaging techniques. Efficient utilization of grid resources requires the development of knowledge-based tools and services that combine domain knowledge with analysis algorithms. In this paper, we first investigate how grid infrastructure can facilitate high-throughput biological imaging research, and present an architecture for providing knowledge-based grid services for this field. We identify two levels of knowledge-based services. The first level provides tools for extracting spatiotemporal knowledge from image sets and the second level provides high-level knowledge management and reasoning services. We then present cellular imaging markup language, an extensible markup language-based language for modeling of biological images and representation of spatiotemporal knowledge. This scheme can be used for spatiotemporal event composition, matching, and automated knowledge extraction and representation for large biological imaging datasets. We demonstrate the expressive power of this formalism by means of different examples and extensive experimental results.

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.

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…

A highly scalable information system as extendable framework solution for medical R&D projects.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Stoll, Regina; Thurow, Kerstin

2009-01-01

For research projects in preventive medicine a flexible information management is needed that offers a free planning and documentation of project specific examinations. The system should allow a simple, preferably automated data acquisition from several distributed sources (e.g., mobile sensors, stationary diagnostic systems, questionnaires, manual inputs) as well as an effective data management, data use and analysis. An information system fulfilling these requirements has been developed at the Center for Life Science Automation (celisca). This system combines data of multiple investigations and multiple devices and displays them on a single screen. The integration of mobile sensor systems for comfortable, location-independent capture of time-based physiological parameter and the possibility of observation of these measurements directly by this system allow new scenarios. The web-based information system presented in this paper is configurable by user interfaces. It covers medical process descriptions, operative process data visualizations, a user-friendly process data processing, modern online interfaces (data bases, web services, XML) as well as a comfortable support of extended data analysis with third-party applications.

ARCHANGEL: Galaxy Photometry System

NASA Astrophysics Data System (ADS)

Schombert, James

2011-07-01

ARCHANGEL is a Unix-based package for the surface photometry of galaxies. While oriented for large angular size systems (i.e. many pixels), its tools can be applied to any imaging data of any size. The package core contains routines to perform the following critical galaxy photometry functions: sky determination; frame cleaning; ellipse fitting; profile fitting; and total and isophotal magnitudes. The goal of the package is to provide an automated, assembly-line type of reduction system for galaxy photometry of space-based or ground-based imaging data. The procedures outlined in the documentation are flux independent, thus, these routines can be used for non-optical data as well as typical imaging datasets. ARCHANGEL has been tested on several current OS's (RedHat Linux, Ubuntu Linux, Solaris, Mac OS X). A tarball for installation is available at the download page. The main routines are Python and FORTRAN based, therefore, a current installation of Python and a FORTRAN compiler are required. The ARCHANGEL package also contains Python hooks to the PGPLOT package, an XML processor and network tools which automatically link to data archives (i.e. NED, HST, 2MASS, etc) to download images in a non-interactive manner.

A Testing Framework for Critical Space SW

NASA Astrophysics Data System (ADS)

Fernandez, Ignacio; Di Cerbo, Antonio; Dehnhardt, Erik; Massimo, Tipaldi; Brünjes, Bernhard

2015-09-01

This paper describes a testing framework for critical space SW named Technical Specification Validation Framework (TSVF). It provides a powerful and flexible means and can be used throughout the SW test activities (test case specification & implementation, test execution and test artifacts analysis). In particular, tests can be run in an automated and/or step-by-step mode. The TSVF framework is currently used for the validation of the Satellite Control Software (SCSW), which runs on the Meteosat Third Generation (MTG) satellite on-board computer. The main purpose of the SCSW is to control the spacecraft along with its various subsystems (AOCS, Payload, Electrical Power, Telemetry Tracking & Command, etc.) in a way that guarantees a high degree of flexibility and autonomy. The TSVF framework serves the challenging needs of the SCSW project, where a plan-driven approach has been combined with an agile process in order to produce preliminary SW versions (with a reduced scope of implemented functionality) in order to fulfill the stakeholders needs ([1]). The paper has been organised as follows. Section 2 gives an overview of the TSVF architecture and interfaces versus the test bench along with the technology used for its implementation. Section 3 describes the key elements of the XML based language for the test case implementation. Section 4 highlights all the benefits compared to conventional test environments requiring a manual test script development, whereas section 5 concludes the paper.

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/).

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.

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.…

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

David, O.

2011-12-01

Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside. While providing all those capabilities, a significant reduction in the size of the model source code was achieved. To support the benefit of annotations for a modeler, studies were conducted to evaluate the effectiveness of an annotation based framework approach with other modeling frameworks and libraries, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A typical hydrological model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks.

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

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.

An ant colony optimization based feature selection for web page classification.

PubMed

Saraç, Esra; Özel, Selma Ayşe

2014-01-01

The increased popularity of the web has caused the inclusion of huge amount of information to the web, and as a result of this explosive information growth, automated web page classification systems are needed to improve search engines' performance. Web pages have a large number of features such as HTML/XML tags, URLs, hyperlinks, and text contents that should be considered during an automated classification process. The aim of this study is to reduce the number of features to be used to improve runtime and accuracy of the classification of web pages. In this study, we used an ant colony optimization (ACO) algorithm to select the best features, and then we applied the well-known C4.5, naive Bayes, and k nearest neighbor classifiers to assign class labels to web pages. We used the WebKB and Conference datasets in our experiments, and we showed that using the ACO for feature selection improves both accuracy and runtime performance of classification. We also showed that the proposed ACO based algorithm can select better features with respect to the well-known information gain and chi square feature selection methods.

Indexing Temporal XML Using FIX

NASA Astrophysics Data System (ADS)

Zheng, Tiankun; Wang, Xinjun; Zhou, Yingchun

XML has become an important criterion for description and exchange of information. It is of practical significance to introduce the temporal information on this basis, because time has penetrated into all walks of life as an important property information .Such kind of database can track document history and recover information to state of any time before, and is called Temporal XML database. We advise a new feature vector on the basis of FIX which is a feature-based XML index, and build an index on temporal XML database using B+ tree, donated TFIX. We also put forward a new query algorithm upon it for temporal query. Our experiments proved that this index has better performance over other kinds of XML indexes. The index can satisfy all TXPath queries with depth up to K(>0).

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.

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.

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

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.

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

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.

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.

Studies in using a universal exchange and inference language for evidence based medicine. Semi-automated learning and reasoning for PICO methodology, systematic review, and environmental epidemiology.

PubMed

Robson, Barry

2016-12-01

The Q-UEL language of XML-like tags and the associated software applications are providing a valuable toolkit for Evidence Based Medicine (EBM). In this paper the already existing applications, data bases, and tags are brought together with new ones. The particular Q-UEL embodiment used here is the BioIngine. The main challenge is one of bringing together the methods of symbolic reasoning and calculative probabilistic inference that underlie EBM and medical decision making. Some space is taken to review this background. The unification is greatly facilitated by Q-UEL's roots in the notation and algebra of Dirac, and by extending Q-UEL into the Wolfram programming environment. Further, the overall problem of integration is also a relatively simple one because of the nature of Q-UEL as a language for interoperability in healthcare and biomedicine, while the notion of workflow is facilitated because of the EBM best practice known as PICO. What remains difficult is achieving a high degree of overall automation because of a well-known difficulty in capturing human expertise in computers: the Feigenbaum bottleneck. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

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…

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…

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

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.

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.

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.

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

Informatics in radiology: automated structured reporting of imaging findings using the AIM standard and XML.

PubMed

Zimmerman, Stefan L; Kim, Woojin; Boonn, William W

2011-01-01

Quantitative and descriptive imaging data are a vital component of the radiology report and are frequently of paramount importance to the ordering physician. Unfortunately, current methods of recording these data in the report are both inefficient and error prone. In addition, the free-text, unstructured format of a radiology report makes aggregate analysis of data from multiple reports difficult or even impossible without manual intervention. A structured reporting work flow has been developed that allows quantitative data created at an advanced imaging workstation to be seamlessly integrated into the radiology report with minimal radiologist intervention. As an intermediary step between the workstation and the reporting software, quantitative and descriptive data are converted into an extensible markup language (XML) file in a standardized format specified by the Annotation and Image Markup (AIM) project of the National Institutes of Health Cancer Biomedical Informatics Grid. The AIM standard was created to allow image annotation data to be stored in a uniform machine-readable format. These XML files containing imaging data can also be stored on a local database for data mining and analysis. This structured work flow solution has the potential to improve radiologist efficiency, reduce errors, and facilitate storage of quantitative and descriptive imaging data for research. Copyright © RSNA, 2011.

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

PubMed

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

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

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

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

Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue

PubMed Central

Bjornsson, Christopher S; Lin, Gang; Al-Kofahi, Yousef; Narayanaswamy, Arunachalam; Smith, Karen L; Shain, William; Roysam, Badrinath

2009-01-01

Brain structural complexity has confounded prior efforts to extract quantitative image-based measurements. We present a systematic ‘divide and conquer’ methodology for analyzing three-dimensional (3D) multi-parameter images of brain tissue to delineate and classify key structures, and compute quantitative associations among them. To demonstrate the method, thick (~100 μm) slices of rat brain tissue were labeled using 3 – 5 fluorescent signals, and imaged using spectral confocal microscopy and unmixing algorithms. Automated 3D segmentation and tracing algorithms were used to delineate cell nuclei, vasculature, and cell processes. From these segmentations, a set of 23 intrinsic and 8 associative image-based measurements was computed for each cell. These features were used to classify astrocytes, microglia, neurons, and endothelial cells. Associations among cells and between cells and vasculature were computed and represented as graphical networks to enable further analysis. The automated results were validated using a graphical interface that permits investigator inspection and corrective editing of each cell in 3D. Nuclear counting accuracy was >89%, and cell classification accuracy ranged from 81–92% depending on cell type. We present a software system named FARSIGHT implementing our methodology. Its output is a detailed XML file containing measurements that may be used for diverse quantitative hypothesis-driven and exploratory studies of the central nervous system. PMID:18294697

MS/MS Automated Selected Ion Chromatograms

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

Monroe, Matthew

2005-12-12

This program can be used to read a LC-MS/MS data file from either a Finnigan ion trap mass spectrometer (.Raw file) or an Agilent Ion Trap mass spectrometer (.MGF and .CDF files) and create a selected ion chromatogram (SIC) for each of the parent ion masses chosen for fragmentation. The largest peak in each SIC is also identified, with reported statistics including peak elution time, height, area, and signal to noise ratio. It creates several output files, including a base peak intensity (BPI) chromatogram for the survey scan, a BPI for the fragmentation scans, an XML file containing the SICmore » data for each parent ion, and a "flat file" (ready for import into a database) containing summaries of the SIC data statistics.« less

NASA Tech Briefs, September 2003

NASA Technical Reports Server (NTRS)

2003-01-01

Topics include: Oxygen-Partial-Pressure Sensor for Aircraft Oxygen Mask; Three-Dimensional Venturi Sensor for Measuring Extreme Winds; Swarms of Micron-Sized Sensors; Monitoring Volcanoes by Use of Air-Dropped Sensor Packages; Capacitive Sensors for Measuring Masses of Cryogenic Fluids; UHF Microstrip Antenna Array for Synthetic- Aperture Radar; Multimode Broad-Band Patch Antennas; 164-GHz MMIC HEMT Frequency Doubler; GPS Position and Heading Circuitry for Ships; Software for Managing Parametric Studies; Software Aids Visualization of Computed Unsteady Flow; Software for Testing Electroactive Structural Components; Advanced Software for Analysis of High-Speed Rolling-Element Bearings; Web Program for Development of GUIs for Cluster Computers; XML-Based Generator of C++ Code for Integration With GUIs; Oxide Protective Coats for Ir/Re Rocket Combustion Chambers; Simplified Waterproofing of Aerogels; Improved Thermal-Insulation Systems for Low Temperatures; Device for Automated Cutting and Transfer of Plant Shoots; Extension of Liouville Formalism to Postinstability Dynamics; Advances in Thrust-Based Emergency Control of an Airplane; Ultrasonic/Sonic Mechanisms for Drilling and Coring; Exercise Device Would Exert Selectable Constant Resistance; Improved Apparatus for Measuring Distance Between Axles; Six Classes of Diffraction-Based Optoelectronic Instruments; Modernizing Fortran 77 Legacy Codes; Active State Model for Autonomous Systems; Shields for Enhanced Protection Against High-Speed Debris; Scaling of Two-Phase Flows to Partial-Earth Gravity; Neutral-Axis Springs for Thin-Wall Integral Boom Hinges.

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.

Automated construction of an intraoperative high-dose-rate treatment plan library for the Varian brachytherapy treatment planning system.

PubMed

Deufel, Christopher L; Furutani, Keith M; Dahl, Robert A; Haddock, Michael G

2016-01-01

The ability to create treatment plans for intraoperative high-dose-rate (IOHDR) brachytherapy is limited by lack of imaging and time constraints. An automated method for creation of a library of high-dose-rate brachytherapy plans that can be used with standard planar applicators in the intraoperative setting is highly desirable. Nonnegative least squares algebraic methods were used to identify dwell time values for flat, rectangular planar applicators. The planar applicators ranged in length and width from 2 cm to 25 cm. Plans were optimized to deliver an absorbed dose of 10 Gy to three different depths from the patient surface: 0 cm, 0.5 cm, and 1.0 cm. Software was written to calculate the optimized dwell times and insert dwell times and positions into a .XML plan template that can be imported into the Varian brachytherapy treatment planning system. The user may import the .XML template into the treatment planning system in the intraoperative setting to match the patient applicator size and prescribed treatment depth. A total of 1587 library plans were created for IOHDR brachytherapy. Median plan generation time was approximately 1 minute per plan. Plan dose was typically 100% ± 1% (mean, standard deviation) of the prescribed dose over the entire length and width of the applicator. Plan uniformity was best for prescription depths of 0 cm and 0.5 cm from the patient surface. An IOHDR plan library may be created using automated methods. Thousands of plan templates may be optimized and prepared in a few hours to accommodate different applicator sizes and treatment depths and reduce treatment planning time. The automated method also enforces dwell time symmetry for symmetrical applicator geometries, which simplifies quality assurance. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

A computational framework for converting textual clinical diagnostic criteria into the quality data model.

PubMed

Hong, Na; Li, Dingcheng; Yu, Yue; Xiu, Qiongying; Liu, Hongfang; Jiang, Guoqian

2016-10-01

Constructing standard and computable clinical diagnostic criteria is an important but challenging research field in the clinical informatics community. The Quality Data Model (QDM) is emerging as a promising information model for standardizing clinical diagnostic criteria. To develop and evaluate automated methods for converting textual clinical diagnostic criteria in a structured format using QDM. We used a clinical Natural Language Processing (NLP) tool known as cTAKES to detect sentences and annotate events in diagnostic criteria. We developed a rule-based approach for assigning the QDM datatype(s) to an individual criterion, whereas we invoked a machine learning algorithm based on the Conditional Random Fields (CRFs) for annotating attributes belonging to each particular QDM datatype. We manually developed an annotated corpus as the gold standard and used standard measures (precision, recall and f-measure) for the performance evaluation. We harvested 267 individual criteria with the datatypes of Symptom and Laboratory Test from 63 textual diagnostic criteria. We manually annotated attributes and values in 142 individual Laboratory Test criteria. The average performance of our rule-based approach was 0.84 of precision, 0.86 of recall, and 0.85 of f-measure; the performance of CRFs-based classification was 0.95 of precision, 0.88 of recall and 0.91 of f-measure. We also implemented a web-based tool that automatically translates textual Laboratory Test criteria into the QDM XML template format. The results indicated that our approaches leveraging cTAKES and CRFs are effective in facilitating diagnostic criteria annotation and classification. Our NLP-based computational framework is a feasible and useful solution in developing diagnostic criteria representation and computerization. Copyright © 2016 Elsevier Inc. All rights reserved.

An Ant Colony Optimization Based Feature Selection for Web Page Classification

PubMed Central

2014-01-01

The increased popularity of the web has caused the inclusion of huge amount of information to the web, and as a result of this explosive information growth, automated web page classification systems are needed to improve search engines' performance. Web pages have a large number of features such as HTML/XML tags, URLs, hyperlinks, and text contents that should be considered during an automated classification process. The aim of this study is to reduce the number of features to be used to improve runtime and accuracy of the classification of web pages. In this study, we used an ant colony optimization (ACO) algorithm to select the best features, and then we applied the well-known C4.5, naive Bayes, and k nearest neighbor classifiers to assign class labels to web pages. We used the WebKB and Conference datasets in our experiments, and we showed that using the ACO for feature selection improves both accuracy and runtime performance of classification. We also showed that the proposed ACO based algorithm can select better features with respect to the well-known information gain and chi square feature selection methods. PMID:25136678

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…

An automated and integrated framework for dust storm detection based on ogc web processing services

NASA Astrophysics Data System (ADS)

Xiao, F.; Shea, G. Y. K.; Wong, M. S.; Campbell, J.

2014-11-01

Dust storms are known to have adverse effects on public health. Atmospheric dust loading is also one of the major uncertainties in global climatic modelling as it is known to have a significant impact on the radiation budget and atmospheric stability. The complexity of building scientific dust storm models is coupled with the scientific computation advancement, ongoing computing platform development, and the development of heterogeneous Earth Observation (EO) networks. It is a challenging task to develop an integrated and automated scheme for dust storm detection that combines Geo-Processing frameworks, scientific models and EO data together to enable the dust storm detection and tracking processes in a dynamic and timely manner. This study develops an automated and integrated framework for dust storm detection and tracking based on the Web Processing Services (WPS) initiated by Open Geospatial Consortium (OGC). The presented WPS framework consists of EO data retrieval components, dust storm detecting and tracking component, and service chain orchestration engine. The EO data processing component is implemented based on OPeNDAP standard. The dust storm detecting and tracking component combines three earth scientific models, which are SBDART model (for computing aerosol optical depth (AOT) of dust particles), WRF model (for simulating meteorological parameters) and HYSPLIT model (for simulating the dust storm transport processes). The service chain orchestration engine is implemented based on Business Process Execution Language for Web Service (BPEL4WS) using open-source software. The output results, including horizontal and vertical AOT distribution of dust particles as well as their transport paths, were represented using KML/XML and displayed in Google Earth. A serious dust storm, which occurred over East Asia from 26 to 28 Apr 2012, is used to test the applicability of the proposed WPS framework. Our aim here is to solve a specific instance of a complex EO data and scientific model integration problem by using a framework and scientific workflow approach together. The experimental result shows that this newly automated and integrated framework can be used to give advance near real-time warning of dust storms, for both environmental authorities and public. The methods presented in this paper might be also generalized to other types of Earth system models, leading to improved ease of use and flexibility.

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 ...

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.

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.

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.

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.

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 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.

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

GlycoExtractor: a web-based interface for high throughput processing of HPLC-glycan data.

PubMed

Artemenko, Natalia V; Campbell, Matthew P; Rudd, Pauline M

2010-04-05

Recently, an automated high-throughput HPLC platform has been developed that can be used to fully sequence and quantify low concentrations of N-linked sugars released from glycoproteins, supported by an experimental database (GlycoBase) and analytical tools (autoGU). However, commercial packages that support the operation of HPLC instruments and data storage lack platforms for the extraction of large volumes of data. The lack of resources and agreed formats in glycomics is now a major limiting factor that restricts the development of bioinformatic tools and automated workflows for high-throughput HPLC data analysis. GlycoExtractor is a web-based tool that interfaces with a commercial HPLC database/software solution to facilitate the extraction of large volumes of processed glycan profile data (peak number, peak areas, and glucose unit values). The tool allows the user to export a series of sample sets to a set of file formats (XML, JSON, and CSV) rather than a collection of disconnected files. This approach not only reduces the amount of manual refinement required to export data into a suitable format for data analysis but also opens the field to new approaches for high-throughput data interpretation and storage, including biomarker discovery and validation and monitoring of online bioprocessing conditions for next generation biotherapeutics.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

An Interface for Specifying Rigid-Body Motions for CFD Applications

NASA Technical Reports Server (NTRS)

Murman, Scott M.; Chan, William; Aftosmis, Michael; Meakin, Robert L.; Kwak, Dochan (Technical Monitor)

2003-01-01

An interface for specifying rigid-body motions for CFD applications is presented. This interface provides a means of describing a component hierarchy in a geometric configuration, as well as the motion (prescribed or six-degree-of-freedom) associated with any component. The interface consists of a general set of datatypes, along with rules for their interaction, and is designed to be flexible in order to evolve as future needs dictate. The specification is currently implemented with an XML file format which is portable across platforms and applications. The motion specification is capable of describing general rigid body motions, and eliminates the need to write and compile new code within the application software for each dynamic configuration, allowing client software to automate dynamic simulations. The interface is integrated with a GUI tool which allows rigid body motions to be prescribed and verified interactively, promoting access to non-expert users. Illustrative examples, as well as the raw XML source of the file specifications, are included.

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.

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.

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.

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…

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…

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.

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.

A Web-Based Framework For a Time-Domain Warehouse

NASA Astrophysics Data System (ADS)

Brewer, J. M.; Bloom, J. S.; Kennedy, R.; Starr, D. L.

2009-09-01

The Berkeley Transients Classification Pipeline (TCP) uses a machine-learning classifier to automatically categorize transients from large data torrents and provide automated notification of astronomical events of scientific interest. As part of the training process, we created a large warehouse of light-curve sources with well-labelled classes that serve as priors to the classification engine. This web-based interactive framework, which we are now making public via DotAstro.org (http://dotastro.org/), allows us to ingest time-variable source data in a wide variety of formats and store it in a common internal data model. Data is passed between pipeline modules in a prototype XML representation of time-series format (VOTimeseries), which can also be emitted to collaborators through dotastro.org. After import, the sources can be visualized using Google Sky, light curves can be inspected interactively, and classifications can be manually adjusted.

Dynamic XML-based exchange of relational data: application to the Human Brain Project.

PubMed

Tang, Zhengming; Kadiyska, Yana; Li, Hao; Suciu, Dan; Brinkley, James F

2003-01-01

This paper discusses an approach to exporting relational data in XML format for data exchange over the web. We describe the first real-world application of SilkRoute, a middleware program that dynamically converts existing relational data to a user-defined XML DTD. The application, called XBrain, wraps SilkRoute in a Java Server Pages framework, thus permitting a web-based XQuery interface to a legacy relational database. The application is demonstrated as a query interface to the University of Washington Brain Project's Language Map Experiment Management System, which is used to manage data about language organization in the brain.

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.

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.

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.

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.

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.

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.

SU-F-T-476: Performance of the AS1200 EPID for Periodic Photon Quality Assurance

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

DeMarco, J; Fraass, B; Yang, W

2016-06-15

Purpose: To assess the dosimetric performance of a new amorphous silicon flat-panel electronic portal imaging device (EPID) suitable for high-intensity, flattening-filter-free delivery mode. Methods: An EPID-based QA suite was created with automation to periodically monitor photon central-axis output and two-dimensional beam profile constancy as a function of gantry angle and dose-rate. A Varian TrueBeamTM linear accelerator installed with Developer Mode was used to customize and deliver XML script routines for the QA suite using the dosimetry mode image acquisition for an aS1200 EPID. Automatic post-processing software was developed to analyze the resulting DICOM images. Results: The EPID was used tomore » monitor photon beam output constancy (central-axis), flatness, and symmetry over a period of 10 months for four photon beam energies (6x, 15x, 6xFFF, and 10xFFF). EPID results were consistent to those measured with a standard daily QA check device. At the four cardinal gantry angles, the standard deviation of the EPID central-axis output was <0.5%. Likewise, EPID measurements were independent for the wide range of dose rates (including up to 2400 mu/min for 10xFFF) studied with a standard deviation of <0.8% relative to the nominal dose rate for each energy. Also, profile constancy and field size measurements showed good agreement with the reference acquisition of 0° gantry angle and nominal dose rate. XML script files were also tested for MU linearity and picket-fence delivery. Using Developer Mode, the test suite was delivered in <60 minutes for all 4 photon energies with 4 dose rates per energy and 5 picket-fence acquisitions. Conclusion: Dosimetry image acquisition using a new EPID was found to be accurate for standard and high-intensity photon beams over a broad range of dose rates over 10 months. Developer Mode provided an efficient platform to customize the EPID acquisitions by using custom script files which significantly reduced the time. This work was funded in part by Varian Medical Systems.« less

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

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.

Introducing ADES: A New IAU Astrometry Data Exchange Standard

NASA Astrophysics Data System (ADS)

Chesley, Steven R.; Hockney, George M.; Holman, Matthew J.

2017-10-01

For several decades, small body astrometry has been exchanged, distributed and archived in the form of 80-column ASCII records. As a replacement for this obsolescent format, we have worked with a number of members of the community to develop the Astrometric Data Exchange Standard (ADES), which was formally adopted by IAU Commission 20 in August 2015 at the XXIX General Assembly in Honolulu, Hawaii.The purpose of ADES is to ensure that useful and available observational information is submitted, archived, and disseminated as needed. Availability of more complete information will allow orbit computers to process the data more correctly, leading to improved accuracy and reliability of orbital fits. In this way, it will be possible to fully exploit the improving accuracy and increasing number of both optical and radar observations. ADES overcomes several limitations of the previous format by allowing characterization of astrometric and photometric errors, adequate precision in time and angle fields, and flexibility and extensibility.To accommodate a diverse base of users, from automated surveys to hands-on follow-up observers, the ADES protocol allows for two file formats, eXtensible Markup Language (XML) and Pipe-Separated Values (PSV). Each format carries the same information and simple tools allow users to losslessly transform back and forth between XML and PSV.We have further developed and refined ADES since it was first announced in July 2015 [1]. The proposal at that time [2] has undergone several modest revisions to aid validation and avoid overloaded fields. We now have validation schema and file transformation utilities. Suitable example files, test suites, and input/output libraries in a number of modern programming languages are now available. Acknowledgements: Useful feedback during the development of ADES has been received from numerous colleagues in the community of observers and orbit specialists working on asteroids comets and planetary satellites. References: [1] Chesley, S.R. (2015) M.P.E.C. 2015-O06. [2] http://minorplanetcenter.net/iau/ info/IAU2015_ADES.pdf

Oak Ridge National Laboratory's (ORNL) Weigh-In-Motion (WIM) Configuration and Data Management Activities

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

Abercrombie, Robert K; Sheldon, Frederick T; Schlicher, Bob G

2006-01-01

The Oak Ridge National Laboratory (ORNL) involvement in the Weigh-in-Motion (WIM) research with both government agencies and private companies dates back to 1989. The discussion here will focus on the US Army's current need for an automated WIM system to weigh and determine the center-of-balance for military wheeled vehicles and cargo and the expanded uses of WIM data. ORNL is addressing configuration and data management issues as they relate to deployments for both military and humanitarian activities. The transition from the previous WIM Gen I to the current Gen II system illustrates a configuration and data management solution that ensuresmore » data integration, integrity, coherence and cost effectiveness. Currently, Army units use portable and fixed scales, tape measures, and calculators to determine vehicle axle, total weights and center of balance for vehicles prior to being transshipped via railcar, ship, or airlifted. Manually weighing and measuring all vehicles subject to these transshipment operations is time-consuming, labor-intensive, hazardous and is prone to human errors (e.g., misreading scales and tape measures, calculating centers of balance and wheel, axle, and vehicle weights, recording data, and transferring data from manually prepared work sheets into an electronic data base and aggravated by adverse weather conditions). Additionally, in the context of the military, the timeliness, safety, success, and effectiveness of airborne heavy-drop operations can be significantly improved by the use of an automated system to weigh and determine center of balance of vehicles while they are in motion. The lack of a standardized airlift-weighing system for joint service use also creates redundant weighing requirements at the cost of scarce resources and time. This case study can be judiciously expanded into commercial operations related to safety and enforcement. The WIM program will provide a means for the Army to automatically identify/weigh and monitor vehicle characteristics for real-time storage/dissemination to the TC-AIMS II (Transportation Coordinators' - Automated Information for Movement System II) for load planning and for providing asset visibility. The WIM system was developed using COTs products and the Reach Back (WIM-RBC) capability is based on a Web-services architecture implemented through best practices of software design (UML and XML schema). Fielded systems and XML-compliant messages can engage the WIM-RBC to store all measurement data in the repository accessible to authorized users through standard secure protocols.« less

CHIME: A Metadata-Based Distributed Software Development Environment

DTIC Science & Technology

2005-01-01

structures by using typography , graphics , and animation. The Software Im- mersion in our conceptual model for CHIME can be seen as a form of Software...Even small- to medium-sized development efforts may involve hundreds of artifacts -- design documents, change requests, test cases and results, code...for managing and organizing information from all phases of the software lifecycle. CHIME is designed around an XML-based metadata architecture, in

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.

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…

Java Application Shell: A Framework for Piecing Together Java Applications

NASA Technical Reports Server (NTRS)

Miller, Philip; Powers, Edward I. (Technical Monitor)

2001-01-01

This session describes the architecture of Java Application Shell (JAS), a Swing-based framework for developing interactive Java applications. Java Application Shell is being developed by Commerce One, Inc. for NASA Goddard Space Flight Center Code 588. The purpose of JAS is to provide a framework for the development of Java applications, providing features that enable the development process to be more efficient, consistent and flexible. Fundamentally, JAS is based upon an architecture where an application is considered a collection of 'plugins'. In turn, a plug-in is a collection of Swing actions defined using XML and packaged in a jar file. Plug-ins may be local to the host platform or remotely-accessible through HTTP. Local and remote plugins are automatically discovered by JAS upon application startup; plugins may also be loaded dynamically without having to re-start the application. Using Extensible Markup Language (XML) to define actions, as opposed to hardcoding them in application logic, allows easier customization of application-specific operations by separating application logic from presentation. Through XML, a developer defines an action that may appear on any number of menus, toolbars, and buttons. Actions maintain and propagate enable/disable states and specify icons, tool-tips, titles, etc. Furthermore, JAS allows actions to be implemented using various scripting languages through the use of IBM's Bean Scripting Framework. Scripted action implementation is seamless to the end-user. In addition to action implementation, scripts may be used for application and unit-level testing. In the case of application-level testing, JAS has hooks to assist a script in simulating end-user input. JAS also provides property and user preference management, JavaHelp, Undo/Redo, Multi-Document Interface, Single-Document Interface, printing, and logging. Finally, Jini technology has also been included into the framework by means of a Jini services browser and the ability to associate services with actions. Several Java technologies have been incorporated into JAS, including Swing, Internal Frames, Java Beans, XML, JavaScript, JavaHelp, and Jini. Additional information is contained in the original extended abstract.

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

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.

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.

CAG - computer-aid-georeferencing, or rapid sharing, restructuring and presentation of environmental data using remote-server georeferencing for the GE clients. Educational and scientific implications.

NASA Astrophysics Data System (ADS)

Hronusov, V. V.

2006-12-01

We suggest a method of using external public servers for rearranging, restructuring and rapid sharing of environmental data for the purpose of quick presentations in numerous GE clients. The method allows to add new philosophy for the presentation (publication) of the data (mostly static) stored in the public domain (e.g., Blue Marble, Visible Earth, etc). - The new approach is generated by publishing freely accessible spreadsheets which contain enough information and links to the data. Due to the fact that most of the large depositories of the data on the environmental monitoring have rather simple net address system as well as simple hierarchy mostly based on the date and type of the data, it is possible to develop the http-based link to the file which contains the data. Publication of new data on the server is recorded by a simple entering a new address into a cell in the spreadsheet. At the moment we use the EditGrid (www.editgrid.com) system as a spreadsheet platform. The generation of kml-codes is achieved on the basis of XML data and XSLT procedures. Since the EditGride environment supports "fetch" and similar commands, it is possible to create"smart-adaptive" KML generation on the fly based on the data streams from RSS and XML sources. The previous GIS-based methods could combine hi-definition data combined from various sources, but large- scale comparisons of dynamic processes have been usually out of reach of the technology. The suggested method allows unlimited number of GE clients to view, review and compare dynamic and static process of previously un-combinable sources, and on unprecedent scales. The ease of automated or computer-assisted georeferencing has already led to translation about 3000 raster public domain imagery, point and linear data sources into GE-language. In addition the suggested method allows a user to create rapid animations to demonstrate dynamic processes; roducts of high demand in education, meteorology, volcanology and potentially in a number of industries. In general it is possible to state that the new approach, which we have tested on numerous projects, saves times and energy in creating huge amounts of georeferenced data of various kinds, and thus provided an excellent tools for education and science.

HDF-EOS 5 Validator

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A computer program partly automates the task of determining whether an HDF-EOS 5 file is valid in that it conforms to specifications for such characteristics as attribute names, dimensionality of data products, and ranges of legal data values. ["HDF-EOS" and variants thereof are defined in "Converting EOS Data From HDF-EOS to netCDF" (GSC-15007-1), which is the first of several preceding articles in this issue of NASA Tech Briefs.] Previously, validity of a file was determined in a tedious and error-prone process in which a person examined human-readable dumps of data-file-format information. The present software helps a user to encode the specifications for an HDFEOS 5 file, and then inspects the file for conformity with the specifications: First, the user writes the specifications in Extensible Markup Language (XML) by use of a document type definition (DTD) that is part of the program. Next, the portion of the program (denoted the validator) that performs the inspection is executed, using, as inputs, the specifications in XML and the HDF-EOS 5 file to be validated. Finally, the user examines the output of the validator.

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.

Online extraction LC-MS/MS method for the simultaneous quantitative confirmation of urine drugs of abuse and metabolites: amphetamines, opiates, cocaine, cannabis, benzodiazepines and methadone.

PubMed

de Jager, Andrew D; Bailey, Neville L

2011-09-01

A rapid LC-MS/MS method for confirmatory testing of five major categories of drugs of abuse (amphetamine-type substances, opiates, cocaine, cannabis metabolites and benzodiazepines) in urine has been developed. All drugs of abuse mandated by the Australian/New Zealand Standard AS/NZS 4308:2008 are quantified in a single chromatographic run. Urine samples are diluted with a mixture of isotope labelled internal standards. An on-line trap-and-flush approach, followed by LC-ESI-MS/MS has been successfully used to process samples in a functioning drugs of abuse laboratory. Following injection of diluted urine samples, compounds retained on the trap cartridge are flushed onto a reverse-phase C18 HPLC column (5-μm particle size) with embedded hydrophylic functionality. A total chromatographic run-time of 15 min is required for adequate resolution. Automated quantitation software algorithms have been developed in-house using XML scripting to partially automate the identification of positive samples, taking into account ion ratio (IR) and retention times (Rt). The sensitivity of the assay was found to be adequate for the quantitation of drugs in urine at and below the confirmation cut-off concentrations prescribed by AS/NZS 4308:2008. Copyright © 2011 Elsevier B.V. All rights reserved.

The Cardiac Safety Research Consortium ECG database.

PubMed

Kligfield, Paul; Green, Cynthia L

2012-01-01

The Cardiac Safety Research Consortium (CSRC) ECG database was initiated to foster research using anonymized, XML-formatted, digitized ECGs with corresponding descriptive variables from placebo- and positive-control arms of thorough QT studies submitted to the US Food and Drug Administration (FDA) by pharmaceutical sponsors. The database can be expanded to other data that are submitted directly to CSRC from other sources, and currently includes digitized ECGs from patients with genotyped varieties of congenital long-QT syndrome; this congenital long-QT database is also linked to ambulatory electrocardiograms stored in the Telemetric and Holter ECG Warehouse (THEW). Thorough QT data sets are available from CSRC for unblinded development of algorithms for analysis of repolarization and for blinded comparative testing of algorithms developed for the identification of moxifloxacin, as used as a positive control in thorough QT studies. Policies and procedures for access to these data sets are available from CSRC, which has developed tools for statistical analysis of blinded new algorithm performance. A recently approved CSRC project will create a data set for blinded analysis of automated ECG interval measurements, whose initial focus will include comparison of four of the major manufacturers of automated electrocardiographs in the United States. CSRC welcomes application for use of the ECG database for clinical investigation. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

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

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.

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

Automated Source-Code-Based Testing of Object-Oriented Software

NASA Astrophysics Data System (ADS)

Gerlich, Ralf; Gerlich, Rainer; Dietrich, Carsten

2014-08-01

With the advent of languages such as C++ and Java in mission- and safety-critical space on-board software, new challenges for testing and specifically automated testing arise. In this paper we discuss some of these challenges, consequences and solutions based on an experiment in automated source- code-based testing for C++.

Technical Note: Direct measurement of continuous TMR data with a 1D tank and automated couch movements.

PubMed

Knutson, Nels C; Schmidt, Matthew C; Belley, Matthew D; Nguyen, Ngoc B; Li, H Harold; Sajo, Erno; Price, Michael J

2017-07-01

Real-time dynamic control of the linear accelerator, couch, and imaging parameters during radiation delivery was investigated as a novel technique for acquiring tissue maximum ratio (TMR) data. TrueBeam Developer Mode (Varian Medical Systems, Palo Alto, CA, USA) was used to control the linear accelerator using the Extensible Markup Language (XML). A single XML file was used to dynamically manipulate the machine, couch, and imaging parameters during radiation delivery. A TG-51 compliant 1D water tank was placed on the treatment couch, and used to position a detector at isocenter at a depth of 24.5 cm. A depth scan was performed towards the water surface. Via XML control, the treatment couch vertical position was simultaneously lowered at the same rate, maintaining the detector position at isocenter, allowing for the collection of TMR data. To ensure the detector remained at isocenter during the delivery, the in-room camera was used to monitor the detector. Continuous kV fluoroscopic images during 10 test runs further confirmed this result. TMR data at multiple Source to Detector Distances (SDD) and scan speeds were acquired to investigate their impact on the TMR data. Percentage depth dose (PDD) scans (for conversion to TMR) along with traditional discrete TMR data were acquired as a standard for comparison. More than 99.8% of the measured points had a gamma value (1%/1 mm) < 1 when compared with discrete or PDD converted TMR data. Fluoroscopic images showed that the concurrent couch and tank movements resulted in SDD errors < 1 mm. TMRs acquired at SDDs of 99, 100, and 101 cm showed differences less than 0.004. TrueBeam Developer Mode was used to collect continuous TMR data with the same accuracy as traditionally collected discrete data, but yielded higher sampled resolution and reduced acquisition time. This novel method does not require the modification of any equipment and does not use a 3D tank or reservoir. © 2017 American Association of Physicists in Medicine.

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

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.

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…

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.

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

Automated audiometry using apple iOS-based application technology.

PubMed

Foulad, Allen; Bui, Peggy; Djalilian, Hamid

2013-11-01

The aim of this study is to determine the feasibility of an Apple iOS-based automated hearing testing application and to compare its accuracy with conventional audiometry. Prospective diagnostic study. Setting Academic medical center. An iOS-based software application was developed to perform automated pure-tone hearing testing on the iPhone, iPod touch, and iPad. To assess for device variations and compatibility, preliminary work was performed to compare the standardized sound output (dB) of various Apple device and headset combinations. Forty-two subjects underwent automated iOS-based hearing testing in a sound booth, automated iOS-based hearing testing in a quiet room, and conventional manual audiometry. The maximum difference in sound intensity between various Apple device and headset combinations was 4 dB. On average, 96% (95% confidence interval [CI], 91%-100%) of the threshold values obtained using the automated test in a sound booth were within 10 dB of the corresponding threshold values obtained using conventional audiometry. When the automated test was performed in a quiet room, 94% (95% CI, 87%-100%) of the threshold values were within 10 dB of the threshold values obtained using conventional audiometry. Under standardized testing conditions, 90% of the subjects preferred iOS-based audiometry as opposed to conventional audiometry. Apple iOS-based devices provide a platform for automated air conduction audiometry without requiring extra equipment and yield hearing test results that approach those of conventional audiometry.

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

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

Nassi-Schneiderman Diagram in HTML Based on AML

ERIC Educational Resources Information Center

Menyhárt, László

2013-01-01

In an earlier work I defined an extension of XML called Algorithm Markup Language (AML) for easy and understandable coding in an IDE which supports XML editing (e.g. NetBeans). The AML extension contains annotations and native language (English or Hungarian) tag names used when coding our algorithm. This paper presents a drawing tool with which…

Text to Speech (TTS) Capabilities for the Common Driver Trainer (CDT)

DTIC Science & Technology

2010-10-01

harnessing in’leigle jalClpeno jocelyn linu ~ los angeles lottery margarine mathematlze mathematized mathematized meme memes memol...including Julie, Kate, and Paul . Based upon the names of the voices, it may be that the VoiceText capability is the technology being used currently on...DFTTSExportToFileEx(O, " Paul ", 1, 1033, "Testing the Digital Future Text-to-Speech SDK.", -1, -1, -1, -1, -1, DFTTS_ TEXT_ TYPE_ XML, "test.wav", 0, "", -1

Enhancing Network Communication in NPSNET-V Virtual Environments Using XML-Described Dynamic Behavior (DBP) Protocols

DTIC Science & Technology

2001-09-01

testing is performed between two machines connected by either a 100 Mbps Ethernet connection or a 56K modem connection. This testing is performed...and defined as follows: • The available bandwidth is set at two different levels (Ethernet 100 Mbps and 56K modem ). 32 • The packet size is set... modem connection. These two connections represent the target 100 Mbps high end and 56k bps low end of anticipated client connections in web-based

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.

Report of official foreign travel to France, June 7--20, 2000

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

J.D. Mason

2000-07-11

The Department of Energy (DOE) has 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 Standardization (ISO) and themore » 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, the authors has 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 his June 2000 trip, he chaired the spring 2000 meeting of SC34 in Paris, France. He also attended a major conference on the use of SGML and XML and led 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 are several SGML-based projects at the Oak Ridge Y-12 Plant. The local project team developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant 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 will use XML to structure its knowledge base. Supporting standards development allows DOE and the Y-12 plant 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 and related topics.« less

An Open Source Tool to Test Interoperability

NASA Astrophysics Data System (ADS)

Bermudez, L. E.

2012-12-01

Scientists interact with information at various levels from gathering of the raw observed data to accessing portrayed processed quality control data. Geoinformatics tools help scientist on the acquisition, storage, processing, dissemination and presentation of geospatial information. Most of the interactions occur in a distributed environment between software components that take the role of either client or server. The communication between components includes protocols, encodings of messages and managing of errors. Testing of these communication components is important to guarantee proper implementation of standards. The communication between clients and servers can be adhoc or follow standards. By following standards interoperability between components increase while reducing the time of developing new software. The Open Geospatial Consortium (OGC), not only coordinates the development of standards but also, within the Compliance Testing Program (CITE), provides a testing infrastructure to test clients and servers. The OGC Web-based Test Engine Facility, based on TEAM Engine, allows developers to test Web services and clients for correct implementation of OGC standards. TEAM Engine is a JAVA open source facility, available at Sourceforge that can be run via command line, deployed in a web servlet container or integrated in developer's environment via MAVEN. The TEAM Engine uses the Compliance Test Language (CTL) and TestNG to test HTTP requests, SOAP services and XML instances against Schemas and Schematron based assertions of any type of web service, not only OGC services. For example, the OGC Web Feature Service (WFS) 1.0.0 test has more than 400 test assertions. Some of these assertions includes conformance of HTTP responses, conformance of GML-encoded data; proper values for elements and attributes in the XML; and, correct error responses. This presentation will provide an overview of TEAM Engine, introduction of how to test via the OGC Testing web site and description of performing local tests. It will also provide information about how to participate in the open source code development of TEAM Engine.

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.

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.

Health Topic XML File Description

MedlinePlus

... description (200 characters maximum) summarizing the page content Example: meta-desc="If you are being tested for Type 2 diabetes, your doctor gives you an A1C test. The test is also used to monitor your ...

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

A DICOM-based 2nd generation Molecular Imaging Data Grid implementing the IHE XDS-i integration profile.

PubMed

Lee, Jasper; Zhang, Jianguo; Park, Ryan; Dagliyan, Grant; Liu, Brent; Huang, H K

2012-07-01

A Molecular Imaging Data Grid (MIDG) was developed to address current informatics challenges in archival, sharing, search, and distribution of preclinical imaging studies between animal imaging facilities and investigator sites. This manuscript presents a 2nd generation MIDG replacing the Globus Toolkit with a new system architecture that implements the IHE XDS-i integration profile. Implementation and evaluation were conducted using a 3-site interdisciplinary test-bed at the University of Southern California. The 2nd generation MIDG design architecture replaces the initial design's Globus Toolkit with dedicated web services and XML-based messaging for dedicated management and delivery of multi-modality DICOM imaging datasets. The Cross-enterprise Document Sharing for Imaging (XDS-i) integration profile from the field of enterprise radiology informatics was adopted into the MIDG design because streamlined image registration, management, and distribution dataflow are likewise needed in preclinical imaging informatics systems as in enterprise PACS application. Implementation of the MIDG is demonstrated at the University of Southern California Molecular Imaging Center (MIC) and two other sites with specified hardware, software, and network bandwidth. Evaluation of the MIDG involves data upload, download, and fault-tolerance testing scenarios using multi-modality animal imaging datasets collected at the USC Molecular Imaging Center. The upload, download, and fault-tolerance tests of the MIDG were performed multiple times using 12 collected animal study datasets. Upload and download times demonstrated reproducibility and improved real-world performance. Fault-tolerance tests showed that automated failover between Grid Node Servers has minimal impact on normal download times. Building upon the 1st generation concepts and experiences, the 2nd generation MIDG system improves accessibility of disparate animal-model molecular imaging datasets to users outside a molecular imaging facility's LAN using a new architecture, dataflow, and dedicated DICOM-based management web services. Productivity and efficiency of preclinical research for translational sciences investigators has been further streamlined for multi-center study data registration, management, and distribution.

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.

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.

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…

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

NASA Astrophysics Data System (ADS)

Fong, Joseph; Cheung, San Kuen

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

An XML-Based Protocol for Distributed Event Services

NASA Technical Reports Server (NTRS)

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

2001-01-01

A recent trend in distributed computing is the construction of high-performance distributed systems called computational grids. One difficulty we have encountered is that there is no standard format for the representation of performance information and no standard protocol for transmitting this information. This limits the types of performance analysis that can be undertaken in complex distributed systems. To address this problem, we present an XML-based protocol for transmitting performance events in distributed systems and evaluate the performance of this protocol.

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.

XML-Based Visual Specification of Multidisciplinary Applications

NASA Technical Reports Server (NTRS)

Al-Theneyan, Ahmed; Jakatdar, Amol; Mehrotra, Piyush; Zubair, Mohammad

2001-01-01

The advancements in the Internet and Web technologies have fueled a growing interest in developing a web-based distributed computing environment. We have designed and developed Arcade, a web-based environment for designing, executing, monitoring, and controlling distributed heterogeneous applications, which is easy to use and access, portable, and provides support through all phases of the application development and execution. A major focus of the environment is the specification of heterogeneous, multidisciplinary applications. In this paper we focus on the visual and script-based specification interface of Arcade. The web/browser-based visual interface is designed to be intuitive to use and can also be used for visual monitoring during execution. The script specification is based on XML to: (1) make it portable across different frameworks, and (2) make the development of our tools easier by using the existing freely available XML parsers and editors. There is a one-to-one correspondence between the visual and script-based interfaces allowing users to go back and forth between the two. To support this we have developed translators that translate a script-based specification to a visual-based specification, and vice-versa. These translators are integrated with our tools and are transparent to users.

Comparison of automated measurements of electrocardiographic intervals and durations by computer-based algorithms of digital electrocardiographs.

PubMed

Kligfield, Paul; Badilini, Fabio; Rowlandson, Ian; Xue, Joel; Clark, Elaine; Devine, Brian; Macfarlane, Peter; de Bie, Johan; Mortara, David; Babaeizadeh, Saeed; Gregg, Richard; Helfenbein, Eric D; Green, Cynthia L

2014-02-01

Automated measurements of electrocardiographic (ECG) intervals are widely used by clinicians for individual patient diagnosis and by investigators in population studies. We examined whether clinically significant systematic differences exist in ECG intervals measured by current generation digital electrocardiographs from different manufacturers and whether differences, if present, are dependent on the degree of abnormality of the selected ECGs. Measurements of RR interval, PR interval, QRS duration, and QT interval were made blindly by 4 major manufacturers of digital electrocardiographs used in the United States from 600 XML files of ECG tracings stored in the US FDA ECG warehouse and released for the purpose of this study by the Cardiac Safety Research Consortium. Included were 3 groups based on expected QT interval and degree of repolarization abnormality, comprising 200 ECGs each from (1) placebo or baseline study period in normal subjects during thorough QT studies, (2) peak moxifloxacin effect in otherwise normal subjects during thorough QT studies, and (3) patients with genotyped variants of congenital long QT syndrome (LQTS). Differences of means between manufacturers were generally small in the normal and moxifloxacin subjects, but in the LQTS patients, differences of means ranged from 2.0 to 14.0 ms for QRS duration and from 0.8 to 18.1 ms for the QT interval. Mean absolute differences between algorithms were similar for QRS duration and QT intervals in the normal and in the moxifloxacin subjects (mean ≤6 ms) but were significantly larger in patients with LQTS. Small but statistically significant group differences in mean interval and duration measurements and means of individual absolute differences exist among automated algorithms of widely used, current generation digital electrocardiographs. Measurement differences, including QRS duration and the QT interval, are greatest for the most abnormal ECGs. © 2014.

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.

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.

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.

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.

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.

Automated population of an i2b2 clinical data warehouse from an openEHR-based data repository.

PubMed

Haarbrandt, Birger; Tute, Erik; Marschollek, Michael

2016-10-01

Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of ∼2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process. Copyright © 2016 Elsevier Inc. All rights reserved.

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

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

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, ...

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.

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.

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 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…

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…

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.

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

Automated Test Case Generation for an Autopilot Requirement Prototype

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Rungta, Neha; Feary, Michael

2011-01-01

Designing safety-critical automation with robust human interaction is a difficult task that is susceptible to a number of known Human-Automation Interaction (HAI) vulnerabilities. It is therefore essential to develop automated tools that provide support both in the design and rapid evaluation of such automation. The Automation Design and Evaluation Prototyping Toolset (ADEPT) enables the rapid development of an executable specification for automation behavior and user interaction. ADEPT supports a number of analysis capabilities, thus enabling the detection of HAI vulnerabilities early in the design process, when modifications are less costly. In this paper, we advocate the introduction of a new capability to model-based prototyping tools such as ADEPT. The new capability is based on symbolic execution that allows us to automatically generate quality test suites based on the system design. Symbolic execution is used to generate both user input and test oracles user input drives the testing of the system implementation, and test oracles ensure that the system behaves as designed. We present early results in the context of a component in the Autopilot system modeled in ADEPT, and discuss the challenges of test case generation in the HAI domain.

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

A PLM-based automated inspection planning system for coordinate measuring machine

NASA Astrophysics Data System (ADS)

Zhao, Haibin; Wang, Junying; Wang, Boxiong; Wang, Jianmei; Chen, Huacheng

2006-11-01

With rapid progress of Product Lifecycle Management (PLM) in manufacturing industry, automatic generation of inspection planning of product and the integration with other activities in product lifecycle play important roles in quality control. But the techniques for these purposes are laggard comparing with techniques of CAD/CAM. Therefore, an automatic inspection planning system for Coordinate Measuring Machine (CMM) was developed to improve the automatization of measuring based on the integration of inspection system in PLM. Feature information representation is achieved based on a PLM canter database; measuring strategy is optimized through the integration of multi-sensors; reasonable number and distribution of inspection points are calculated and designed with the guidance of statistic theory and a synthesis distribution algorithm; a collision avoidance method is proposed to generate non-collision inspection path with high efficiency. Information mapping is performed between Neutral Interchange Files (NIFs), such as STEP, DML, DMIS, XML, etc., to realize information integration with other activities in the product lifecycle like design, manufacturing and inspection execution, etc. Simulation was carried out to demonstrate the feasibility of the proposed system. As a result, the inspection process is becoming simpler and good result can be got based on the integration in PLM.

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…

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

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

Paul Jehn; Mike Stettner

GWPC, DOGGR, and other state agencies propose to build eBusiness applications based on a .NET front-end user interface for the DOE's Energy 100 Award-winning Risk Based Data Management System (RBDMS) data source and XML Web services. This project will slash the costs of regulatory compliance by automating routine regulatory reporting and permit notice review and by making it easier to exchange data with the oil and gas industry--especially small, independent operators. Such operators, who often do not have sophisticated in-house databases, will be able to use a subset of the same RBDMS tools available to the agencies on the desktopmore » to file permit notices and production reports online. Once the data passes automated quality control checks, the application will upload the data into the agency's RBDMS data source. The operators also will have access to state agency datasets to focus exploration efforts and to perform production forecasting, economic evaluations, and risk assessments. With the ability to identify economically feasible oil and gas prospects, including unconventional plays, over the Internet, operators will minimize travel and other costs. Because GWPC will coordinate these data sharing efforts with the Bureau of Land Management (BLM), this project will improve access to public lands and make strides towards reducing the duplicative reporting to which industry is now subject for leases that cross jurisdictions. The resulting regulatory streamlining and improved access to agency data will make more domestic oil and gas available to the American public while continuing to safeguard environmental assets.« less

Generic and Automated Data Evaluation in Analytical Measurement.

PubMed

Adam, Martin; Fleischer, Heidi; Thurow, Kerstin

2017-04-01

In the past year, automation has become more and more important in the field of elemental and structural chemical analysis to reduce the high degree of manual operation and processing time as well as human errors. Thus, a high number of data points are generated, which requires fast and automated data evaluation. To handle the preprocessed export data from different analytical devices with software from various vendors offering a standardized solution without any programming knowledge should be preferred. In modern laboratories, multiple users will use this software on multiple personal computers with different operating systems (e.g., Windows, Macintosh, Linux). Also, mobile devices such as smartphones and tablets have gained growing importance. The developed software, Project Analytical Data Evaluation (ADE), is implemented as a web application. To transmit the preevaluated data from the device software to the Project ADE, the exported XML report files are detected and the included data are imported into the entities database using the Data Upload software. Different calculation types of a sample within one measurement series (e.g., method validation) are identified using information tags inside the sample name. The results are presented in tables and diagrams on different information levels (general, detailed for one analyte or sample).

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).

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

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

XSemantic: An Extension of LCA Based XML Semantic Search

NASA Astrophysics Data System (ADS)

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

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

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.

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,…

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.

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.

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

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.

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.

Multipurpose Controller with EPICS integration and data logging: BPM application for ESS Bilbao

NASA Astrophysics Data System (ADS)

Arredondo, I.; del Campo, M.; Echevarria, P.; Jugo, J.; Etxebarria, V.

2013-10-01

This work presents a multipurpose configurable control system which can be integrated in an EPICS control network, this functionality being configured through a XML configuration file. The core of the system is the so-called Hardware Controller which is in charge of the control hardware management, the set up and communication with the EPICS network and the data storage. The reconfigurable nature of the controller is based on a single XML file, allowing any final user to easily modify and adjust the control system to any specific requirement. The selected Java development environment ensures a multiplatform operation and large versatility, even regarding the control hardware to be controlled. Specifically, this paper, focused on fast control based on a high performance FPGA, describes also an application approach for the ESS Bilbao's Beam Position Monitoring system. The implementation of the XML configuration file and the satisfactory performance outcome achieved are presented, as well as a general description of the Multipurpose Controller itself.

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

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

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…

Virtual Network Configuration Management System for Data Center Operations and Management

NASA Astrophysics Data System (ADS)

Okita, Hideki; Yoshizawa, Masahiro; Uehara, Keitaro; Mizuno, Kazuhiko; Tarui, Toshiaki; Naono, Ken

Virtualization technologies are widely deployed in data centers to improve system utilization. However, they increase the workload for operators, who have to manage the structure of virtual networks in data centers. A virtual-network management system which automates the integration of the configurations of the virtual networks is provided. The proposed system collects the configurations from server virtualization platforms and VLAN-supported switches, and integrates these configurations according to a newly developed XML-based management information model for virtual-network configurations. Preliminary evaluations show that the proposed system helps operators by reducing the time to acquire the configurations from devices and correct the inconsistency of operators' configuration management database by about 40 percent. Further, they also show that the proposed system has excellent scalability; the system takes less than 20 minutes to acquire the virtual-network configurations from a large scale network that includes 300 virtual machines. These results imply that the proposed system is effective for improving the configuration management process for virtual networks in data centers.

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.

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

Trick Simulation Environment 07

NASA Technical Reports Server (NTRS)

Lin, Alexander S.; Penn, John M.

2012-01-01

The Trick Simulation Environment is a generic simulation toolkit used for constructing and running simulations. This release includes a Monte Carlo analysis simulation framework and a data analysis package. It produces all auto documentation in XML. Also, the software is capable of inserting a malfunction at any point during the simulation. Trick 07 adds variable server output options and error messaging and is capable of using and manipulating wide characters for international support. Wide character strings are available as a fundamental type for variables processed by Trick. A Trick Monte Carlo simulation uses a statistically generated, or predetermined, set of inputs to iteratively drive the simulation. Also, there is a framework in place for optimization and solution finding where developers may iteratively modify the inputs per run based on some analysis of the outputs. The data analysis package is capable of reading data from external simulation packages such as MATLAB and Octave, as well as the common comma-separated values (CSV) format used by Excel, without the use of external converters. The file formats for MATLAB and Octave were obtained from their documentation sets, and Trick maintains generic file readers for each format. XML tags store the fields in the Trick header comments. For header files, XML tags for structures and enumerations, and the members within are stored in the auto documentation. For source code files, XML tags for each function and the calling arguments are stored in the auto documentation. When a simulation is built, a top level XML file, which includes all of the header and source code XML auto documentation files, is created in the simulation directory. Trick 07 provides an XML to TeX converter. The converter reads in header and source code XML documentation files and converts the data to TeX labels and tables suitable for inclusion in TeX documents. A malfunction insertion capability allows users to override the value of any simulation variable, or call a malfunction job, at any time during the simulation. Users may specify conditions, use the return value of a malfunction trigger job, or manually activate a malfunction. The malfunction action may consist of executing a block of input file statements in an action block, setting simulation variable values, call a malfunction job, or turn on/off simulation jobs.

VSDMIP: virtual screening data management on an integrated platform

NASA Astrophysics Data System (ADS)

Gil-Redondo, Rubén; Estrada, Jorge; Morreale, Antonio; Herranz, Fernando; Sancho, Javier; Ortiz, Ángel R.

2009-03-01

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

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

Compressing Aviation Data in XML Format

NASA Technical Reports Server (NTRS)

Patel, Hemil; Lau, Derek; Kulkarni, Deepak

2003-01-01

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

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.

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.

TOMML: A Rule Language for Structured Data

NASA Astrophysics Data System (ADS)

Cirstea, Horatiu; Moreau, Pierre-Etienne; Reilles, Antoine

We present the TOM language that extends JAVA with the purpose of providing high level constructs inspired by the rewriting community. TOM bridges thus the gap between a general purpose language and high level specifications based on rewriting. This approach was motivated by the promotion of rule based techniques and their integration in large scale applications. Powerful matching capabilities along with a rich strategy language are among TOM's strong features that make it easy to use and competitive with respect to other rule based languages. TOM is thus a natural choice for querying and transforming structured data and in particular XML documents [1]. We present here its main XML oriented features and illustrate its use on several examples.

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

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.

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.

DbMap: improving database interoperability issues in medical software using a simple, Java-Xml based solution.

PubMed Central

Karadimas, H.; Hemery, F.; Roland, P.; Lepage, E.

2000-01-01

In medical software development, the use of databases plays a central role. However, most of the databases have heterogeneous encoding and data models. To deal with these variations in the application code directly is error-prone and reduces the potential reuse of the produced software. Several approaches to overcome these limitations have been proposed in the medical database literature, which will be presented. We present a simple solution, based on a Java library, and a central Metadata description file in XML. This development approach presents several benefits in software design and development cycles, the main one being the simplicity in maintenance. PMID:11079915

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 .

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

PubMed

Griss, Johannes; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan Antonio

2012-03-01

We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used in conjunction with mzIdentML, the recently released standard data format for reporting protein and peptide identifications, developed by the HUPO proteomics standards initiative (PSI). mzIdentML files do not contain spectra data but contain references to different kinds of external MS data files. As a key functionality, all parsers implement a common interface that supports the various methods used by mzIdentML to reference external spectra. Thus, when developing software for mzIdentML, programmers no longer have to support multiple MS data file formats but only this one interface. The library (which includes a viewer) is open source and, together with detailed documentation, can be downloaded from http://code.google.com/p/jmzreader/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Association between fully automated MRI-based volumetry of different brain regions and neuropsychological test performance in patients with amnestic mild cognitive impairment and Alzheimer's disease.

PubMed

Arlt, Sönke; Buchert, Ralph; Spies, Lothar; Eichenlaub, Martin; Lehmbeck, Jan T; Jahn, Holger

2013-06-01

Fully automated magnetic resonance imaging (MRI)-based volumetry may serve as biomarker for the diagnosis in patients with mild cognitive impairment (MCI) or dementia. We aimed at investigating the relation between fully automated MRI-based volumetric measures and neuropsychological test performance in amnestic MCI and patients with mild dementia due to Alzheimer's disease (AD) in a cross-sectional and longitudinal study. In order to assess a possible prognostic value of fully automated MRI-based volumetry for future cognitive performance, the rate of change of neuropsychological test performance over time was also tested for its correlation with fully automated MRI-based volumetry at baseline. In 50 subjects, 18 with amnestic MCI, 21 with mild AD, and 11 controls, neuropsychological testing and T1-weighted MRI were performed at baseline and at a mean follow-up interval of 2.1 ± 0.5 years (n = 19). Fully automated MRI volumetry of the grey matter volume (GMV) was performed using a combined stereotactic normalisation and segmentation approach as provided by SPM8 and a set of pre-defined binary lobe masks. Left and right hippocampus masks were derived from probabilistic cytoarchitectonic maps. Volumes of the inner and outer liquor space were also determined automatically from the MRI. Pearson's test was used for the correlation analyses. Left hippocampal GMV was significantly correlated with performance in memory tasks, and left temporal GMV was related to performance in language tasks. Bilateral frontal, parietal and occipital GMVs were correlated to performance in neuropsychological tests comprising multiple domains. Rate of GMV change in the left hippocampus was correlated with decline of performance in the Boston Naming Test (BNT), Mini-Mental Status Examination, and trail making test B (TMT-B). The decrease of BNT and TMT-A performance over time correlated with the loss of grey matter in multiple brain regions. We conclude that fully automated MRI-based volumetry allows detection of regional grey matter volume loss that correlates with neuropsychological performance in patients with amnestic MCI or mild AD. Because of the high level of automation, MRI-based volumetry may easily be integrated into clinical routine to complement the current diagnostic procedure.

Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

2006-12-01

Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

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 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.

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.

Adopting and adapting a commercial view of web services for the Navy

NASA Astrophysics Data System (ADS)

Warner, Elizabeth; Ladner, Roy; Katikaneni, Uday; Petry, Fred

2005-05-01

Web Services are being adopted as the enabling technology to provide net-centric capabilities for many Department of Defense operations. The Navy Enterprise Portal, for example, is Web Services-based, and the Department of the Navy is promulgating guidance for developing Web Services. Web Services, however, only constitute a baseline specification that provides the foundation on which users, under current approaches, write specialized applications in order to retrieve data over the Internet. Application development may increase dramatically as the number of different available Web Services increases. Reasons for specialized application development include XML schema versioning differences, adoption/use of diverse business rules, security access issues, and time/parameter naming constraints, among others. We are currently developing for the US Navy a system which will improve delivery of timely and relevant meteorological and oceanographic (MetOc) data to the warfighter. Our objective is to develop an Advanced MetOc Broker (AMB) that leverages Web Services technology to identify, retrieve and integrate relevant MetOc data in an automated manner. The AMB will utilize a Mediator, which will be developed by applying ontological research and schema matching techniques to MetOc forms of data. The AMB, using the Mediator, will support a new, advanced approach to the use of Web Services; namely, the automated identification, retrieval and integration of MetOc data. Systems based on this approach will then not require extensive end-user application development for each Web Service from which data can be retrieved. Users anywhere on the globe will be able to receive timely environmental data that fits their particular needs.

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.

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.

"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…

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

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.

Automatic page layout using genetic algorithms for electronic albuming

NASA Astrophysics Data System (ADS)

Geigel, Joe; Loui, Alexander C. P.

2000-12-01

In this paper, we describe a flexible system for automatic page layout that makes use of genetic algorithms for albuming applications. The system is divided into two modules, a page creator module which is responsible for distributing images amongst various album pages, and an image placement module which positions images on individual pages. Final page layouts are specified in a textual form using XML for printing or viewing over the Internet. The system makes use of genetic algorithms, a class of search and optimization algorithms that are based on the concepts of biological evolution, for generating solutions with fitness based on graphic design preferences supplied by the user. The genetic page layout algorithm has been incorporated into a web-based prototype system for interactive page layout over the Internet. The prototype system is built using client-server architecture and is implemented in java. The system described in this paper has demonstrated the feasibility of using genetic algorithms for automated page layout in albuming and web-based imaging applications. We believe that the system adequately proves the validity of the concept, providing creative layouts in a reasonable number of iterations. By optimizing the layout parameters of the fitness function, we hope to further improve the quality of the final layout in terms of user preference and computation speed.

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

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

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.

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.…

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

MER Telemetry Processor

NASA Technical Reports Server (NTRS)

Lee, Hyun H.

2012-01-01

MERTELEMPROC processes telemetered data in data product format and generates Experiment Data Records (EDRs) for many instruments (HAZCAM, NAVCAM, PANCAM, microscopic imager, Moessbauer spectrometer, APXS, RAT, and EDLCAM) on the Mars Exploration Rover (MER). If the data is compressed, then MERTELEMPROC decompresses the data with an appropriate decompression algorithm. There are two compression algorithms (ICER and LOCO) used in MER. This program fulfills a MER specific need to generate Level 1 products within a 60-second time requirement. EDRs generated by this program are used by merinverter, marscahv, marsrad, and marsjplstereo to generate higher-level products for the mission operations. MERTELEPROC was the first GDS program to process the data product. Metadata of the data product is in XML format. The software allows user-configurable input parameters, per-product processing (not streambased processing), and fail-over is allowed if the leading image header is corrupted. It is used within the MER automated pipeline. MERTELEMPROC is part of the OPGS (Operational Product Generation Subsystem) automated pipeline, which analyzes images returned by in situ spacecraft and creates level 1 products to assist in operations, science, and outreach.

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…

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…

Hierarchy Software Development Framework (h-dp-fwk) project

NASA Astrophysics Data System (ADS)

Zaytsev, A.

2010-04-01

Hierarchy Software Development Framework provides a lightweight tool for building portable modular applications for performing automated data analysis tasks in a batch mode. The history of design and development activities devoted to the project has begun in March 2005 and from the very beginning it was targeting the case of building experimental data processing applications for the CMD-3 experiment which is being commissioned at Budker Institute of Nuclear Physics (BINP, Novosibirsk, Russia). Its design addresses the generic case of modular data processing application operating within the well defined distributed computing environment. The main features of the framework are modularity, built-in message and data exchange mechanisms, XInclude and XML schema enabled XML configuration management tools, dedicated log management tools, internal debugging tools, both dynamic and static module chains support, internal DSO version and consistency checking, well defined API for developing specialized frameworks. It is supported on Scientific Linux 4 and 5 and planned to be ported to other platforms as well. The project is provided with the comprehensive set of technical documentation and users' guides. The licensing schema for the source code, binaries and documentation implies that the product is free for non-commercial use. Although the development phase is not over and many features are to be implemented yet the project is considered ready for public use and creating applications in various fields including development of events reconstruction software for small and moderate scale HEP experiments.

Partial Automation of Requirements Tracing

NASA Technical Reports Server (NTRS)

Hayes, Jane; Dekhtyar, Alex; Sundaram, Senthil; Vadlamudi, Sravanthi

2006-01-01

Requirements Tracing on Target (RETRO) is software for after-the-fact tracing of textual requirements to support independent verification and validation of software. RETRO applies one of three user-selectable information-retrieval techniques: (1) term frequency/inverse document frequency (TF/IDF) vector retrieval, (2) TF/IDF vector retrieval with simple thesaurus, or (3) keyword extraction. One component of RETRO is the graphical user interface (GUI) for use in initiating a requirements-tracing project (a pair of artifacts to be traced to each other, such as a requirements spec and a design spec). Once the artifacts have been specified and the IR technique chosen, another component constructs a representation of the artifact elements and stores it on disk. Next, the IR technique is used to produce a first list of candidate links (potential matches between the two artifact levels). This list, encoded in Extensible Markup Language (XML), is optionally processed by a filtering component designed to make the list somewhat smaller without sacrificing accuracy. Through the GUI, the user examines a number of links and returns decisions (yes, these are links; no, these are not links). Coded in XML, these decisions are provided to a "feedback processor" component that prepares the data for the next application of the IR technique. The feedback reduces the incidence of erroneous candidate links. Unlike related prior software, RETRO does not require the user to assign keywords, and automatically builds a document index.

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

PubMed

Panahiazar, Maryam; Sheth, Amit P; Ranabahu, Ajith; Vos, Rutger A; Leebens-Mack, Jim

2013-01-01

Phylogenetic analyses can resolve historical relationships among genes, organisms or higher taxa. Understanding such relationships can elucidate a wide range of biological phenomena, including, for example, the importance of gene and genome duplications in the evolution of gene function, the role of adaptation as a driver of diversification, or the evolutionary consequences of biogeographic shifts. Phyloinformaticists are developing data standards, databases and communication protocols (e.g. Application Programming Interfaces, APIs) to extend the accessibility of gene trees, species trees, and the metadata necessary to interpret these trees, thus enabling researchers across the life sciences to reuse phylogenetic knowledge. Specifically, Semantic Web technologies are being developed to make phylogenetic knowledge interpretable by web agents, thereby enabling intelligently automated, high-throughput reuse of results generated by phylogenetic research. This manuscript describes an ontology-driven, semantic problem-solving environment for phylogenetic analyses and introduces artefacts that can promote phyloinformatic efforts to promote accessibility of trees and underlying metadata. PhylOnt is an extensible ontology with concepts describing tree types and tree building methodologies including estimation methods, models and programs. In addition we present the PhylAnt platform for annotating scientific articles and NeXML files with PhylOnt concepts. The novelty of this work is the annotation of NeXML files and phylogenetic related documents with PhylOnt Ontology. This approach advances data reuse in phyloinformatics.

Automated Portable Test System (APTS) - A performance envelope assessment tool

NASA Technical Reports Server (NTRS)

Kennedy, R. S.; Dunlap, W. P.; Jones, M. B.; Wilkes, R. L.; Bittner, A. C., Jr.

1985-01-01

The reliability and stability of microcomputer-based psychological tests are evaluated. The hardware, test programs, and system control of the Automated Portable Test System, which assesses human performance and subjective status, are described. Subjects were administered 11 pen-and-pencil and microcomputer-based tests for 10 sessions. The data reveal that nine of the 10 tests stabilized by the third administration; inertial correlations were high and consistent. It is noted that the microcomputer-based tests display good psychometric properties in terms of differential stability and reliability.

The Pediatric Emergency Care Applied Research Network Registry: A Multicenter Electronic Health Record Registry of Pediatric Emergency Care.

PubMed

Deakyne Davies, Sara J; Grundmeier, Robert W; Campos, Diego A; Hayes, Katie L; Bell, Jamie; Alessandrini, Evaline A; Bajaj, Lalit; Chamberlain, James M; Gorelick, Marc H; Enriquez, Rene; Casper, T Charles; Scheid, Beth; Kittick, Marlena; Dean, J Michael; Alpern, Elizabeth R

2018-04-01

 Electronic health record (EHR)-based registries allow for robust data to be derived directly from the patient clinical record and can provide important information about processes of care delivery and patient health outcomes.  A data dictionary, and subsequent data model, were developed describing EHR data sources to include all processes of care within the emergency department (ED). ED visit data were deidentified and XML files were created and submitted to a central data coordinating center for inclusion in the registry. Automated data quality control occurred prior to submission through an application created for this project. Data quality reports were created for manual data quality review.  The Pediatric Emergency Care Applied Research Network (PECARN) Registry, representing four hospital systems and seven EDs, demonstrates that ED data from disparate health systems and EHR vendors can be harmonized for use in a single registry with a common data model. The current PECARN Registry represents data from 2,019,461 pediatric ED visits, 894,503 distinct patients, more than 12.5 million narrative reports, and 12,469,754 laboratory tests and continues to accrue data monthly.  The Registry is a robust harmonized clinical registry that includes data from diverse patients, sites, and EHR vendors derived via data extraction, deidentification, and secure submission to a central data coordinating center. The data provided may be used for benchmarking, clinical quality improvement, and comparative effectiveness research. Schattauer.

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.

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

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/.

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

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.

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.

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.

Testing Strategies for Model-Based Development

NASA Technical Reports Server (NTRS)

Heimdahl, Mats P. E.; Whalen, Mike; Rajan, Ajitha; Miller, Steven P.

2006-01-01

This report presents an approach for testing artifacts generated in a model-based development process. This approach divides the traditional testing process into two parts: requirements-based testing (validation testing) which determines whether the model implements the high-level requirements and model-based testing (conformance testing) which determines whether the code generated from a model is behaviorally equivalent to the model. The goals of the two processes differ significantly and this report explores suitable testing metrics and automation strategies for each. To support requirements-based testing, we define novel objective requirements coverage metrics similar to existing specification and code coverage metrics. For model-based testing, we briefly describe automation strategies and examine the fault-finding capability of different structural coverage metrics using tests automatically generated from the model.

The tissue microarray data exchange specification: A document type definition to validate and enhance XML data

PubMed Central

Nohle, David G; Ayers, Leona W

2005-01-01

Background The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness. Results A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE). Conclusion ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data. PMID:15871741

Automation of diagnostic genetic testing: mutation detection by cyclic minisequencing.

PubMed

Alagrund, Katariina; Orpana, Arto K

2014-01-01

The rising role of nucleic acid testing in clinical decision making is creating a need for efficient and automated diagnostic nucleic acid test platforms. Clinical use of nucleic acid testing sets demands for shorter turnaround times (TATs), lower production costs and robust, reliable methods that can easily adopt new test panels and is able to run rare tests in random access principle. Here we present a novel home-brew laboratory automation platform for diagnostic mutation testing. This platform is based on the cyclic minisequecing (cMS) and two color near-infrared (NIR) detection. Pipetting is automated using Tecan Freedom EVO pipetting robots and all assays are performed in 384-well micro plate format. The automation platform includes a data processing system, controlling all procedures, and automated patient result reporting to the hospital information system. We have found automated cMS a reliable, inexpensive and robust method for nucleic acid testing for a wide variety of diagnostic tests. The platform is currently in clinical use for over 80 mutations or polymorphisms. Additionally to tests performed from blood samples, the system performs also epigenetic test for the methylation of the MGMT gene promoter, and companion diagnostic tests for analysis of KRAS and BRAF gene mutations from formalin fixed and paraffin embedded tumor samples. Automation of genetic test reporting is found reliable and efficient decreasing the work load of academic personnel.

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

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.

Black-Box System Testing of Real-Time Embedded Systems Using Random and Search-Based Testing

NASA Astrophysics Data System (ADS)

Arcuri, Andrea; Iqbal, Muhammad Zohaib; Briand, Lionel

Testing real-time embedded systems (RTES) is in many ways challenging. Thousands of test cases can be potentially executed on an industrial RTES. Given the magnitude of testing at the system level, only a fully automated approach can really scale up to test industrial RTES. In this paper we take a black-box approach and model the RTES environment using the UML/MARTE international standard. Our main motivation is to provide a more practical approach to the model-based testing of RTES by allowing system testers, who are often not familiar with the system design but know the application domain well-enough, to model the environment to enable test automation. Environment models can support the automation of three tasks: the code generation of an environment simulator, the selection of test cases, and the evaluation of their expected results (oracles). In this paper, we focus on the second task (test case selection) and investigate three test automation strategies using inputs from UML/MARTE environment models: Random Testing (baseline), Adaptive Random Testing, and Search-Based Testing (using Genetic Algorithms). Based on one industrial case study and three artificial systems, we show how, in general, no technique is better than the others. Which test selection technique to use is determined by the failure rate (testing stage) and the execution time of test cases. Finally, we propose a practical process to combine the use of all three test strategies.

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.

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"…

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)

Automated Low-Cost Smartphone-Based Lateral Flow Saliva Test Reader for Drugs-of-Abuse Detection.

PubMed

Carrio, Adrian; Sampedro, Carlos; Sanchez-Lopez, Jose Luis; Pimienta, Miguel; Campoy, Pascual

2015-11-24

Lateral flow assay tests are nowadays becoming powerful, low-cost diagnostic tools. Obtaining a result is usually subject to visual interpretation of colored areas on the test by a human operator, introducing subjectivity and the possibility of errors in the extraction of the results. While automated test readers providing a result-consistent solution are widely available, they usually lack portability. In this paper, we present a smartphone-based automated reader for drug-of-abuse lateral flow assay tests, consisting of an inexpensive light box and a smartphone device. Test images captured with the smartphone camera are processed in the device using computer vision and machine learning techniques to perform automatic extraction of the results. A deep validation of the system has been carried out showing the high accuracy of the system. The proposed approach, applicable to any line-based or color-based lateral flow test in the market, effectively reduces the manufacturing costs of the reader and makes it portable and massively available while providing accurate, reliable results.

Technical Note: A Feasibility Study of Using the Flat Panel Detector on Linac for the kV X-ray Generator Test.

PubMed

Cai, Bin; Dolly, Steven; Kamal, Gregory; Yaddanapudi, Sridhar; Sun, Baozhou; Goddu, S Murty; Mutic, Sasa; Li, Hua

2018-04-28

To investigate the feasibility of using kV flat panel detector on linac for consistency evaluations of kV X-ray generator performance. An in-house designed aluminum (Al) array phantom with six 9×9 cm 2 square regions having various thickness was proposed and used in this study. Through XML script-driven image acquisition, kV images with various acquisition settings were obtained using the kV flat panel detector. Utilizing pre-established baseline curves, the consistency of X-ray tube output characteristics including tube voltage accuracy, exposure accuracy and exposure linearity were assessed through image quality assessment metrics including ROI mean intensity, ROI standard deviation (SD) and noise power spectrums (NPS). The robustness of this method was tested on two linacs for a three-month period. With the proposed method, tube voltage accuracy can be verified through conscience check with a 2% tolerance and 2 kVp intervals for forty different kVp settings. The exposure accuracy can be tested with a 4% consistency tolerance for three mAs settings over forty kVp settings. The exposure linearity tested with three mAs settings achieved a coefficient of variation (CV) of 0.1. We proposed a novel approach that uses the kV flat panel detector available on linac for X-ray generator test. This approach eliminates the inefficiencies and variability associated with using third party QA detectors while enabling an automated process. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Testing primates with joystick-based automated apparatus - Lessons from the Language Research Center's Computerized Test System

NASA Technical Reports Server (NTRS)

Washburn, David A.; Rumbaugh, Duane M.

1992-01-01

Nonhuman primates provide useful models for studying a variety of medical, biological, and behavioral topics. Four years of joystick-based automated testing of monkeys using the Language Research Center's Computerized Test System (LRC-CTS) are examined to derive hints and principles for comparable testing with other species - including humans. The results of multiple parametric studies are reviewed, and reliability data are presented to reveal the surprises and pitfalls associated with video-task testing of performance.

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.

Common data model for natural language processing based on two existing standard information models: CDA+GrAF.

PubMed

Meystre, Stéphane M; Lee, Sanghoon; Jung, Chai Young; Chevrier, Raphaël D

2012-08-01

An increasing need for collaboration and resources sharing in the Natural Language Processing (NLP) research and development community motivates efforts to create and share a common data model and a common terminology for all information annotated and extracted from clinical text. We have combined two existing standards: the HL7 Clinical Document Architecture (CDA), and the ISO Graph Annotation Format (GrAF; in development), to develop such a data model entitled "CDA+GrAF". We experimented with several methods to combine these existing standards, and eventually selected a method wrapping separate CDA and GrAF parts in a common standoff annotation (i.e., separate from the annotated text) XML document. Two use cases, clinical document sections, and the 2010 i2b2/VA NLP Challenge (i.e., problems, tests, and treatments, with their assertions and relations), were used to create examples of such standoff annotation documents, and were successfully validated with the XML schemata provided with both standards. We developed a tool to automatically translate annotation documents from the 2010 i2b2/VA NLP Challenge format to GrAF, and automatically generated 50 annotation documents using this tool, all successfully validated. Finally, we adapted the XSL stylesheet provided with HL7 CDA to allow viewing annotation XML documents in a web browser, and plan to adapt existing tools for translating annotation documents between CDA+GrAF and the UIMA and GATE frameworks. This common data model may ease directly comparing NLP tools and applications, combining their output, transforming and "translating" annotations between different NLP applications, and eventually "plug-and-play" of different modules in NLP applications. Copyright © 2011 Elsevier Inc. All rights reserved.

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+.

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…

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.

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/.

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.

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 SSM/PMAD automated test bed project

NASA Technical Reports Server (NTRS)

Lollar, Louis F.

1991-01-01

The Space Station Module/Power Management and Distribution (SSM/PMAD) autonomous subsystem project was initiated in 1984. The project's goal has been to design and develop an autonomous, user-supportive PMAD test bed simulating the SSF Hab/Lab module(s). An eighteen kilowatt SSM/PMAD test bed model with a high degree of automated operation has been developed. This advanced automation test bed contains three expert/knowledge based systems that interact with one another and with other more conventional software residing in up to eight distributed 386-based microcomputers to perform the necessary tasks of real-time and near real-time load scheduling, dynamic load prioritizing, and fault detection, isolation, and recovery (FDIR).

Automatic Indexing for Content Analysis of Whale Recordings and XML Representation

NASA Astrophysics Data System (ADS)

Bénard, Frédéric; Glotin, Hervé

2010-12-01

This paper focuses on the robust indexing of sperm whale hydrophone recordings based on a set of features extracted from a real-time passive underwater acoustic tracking algorithm for multiple whales using four hydrophones. Acoustic localization permits the study of whale behavior in deep water without interfering with the environment. Given the position coordinates, we are able to generate different features such as the speed, energy of the clicks, Inter-Click-Interval (ICI), and so on. These features allow to construct different markers which allow us to index and structure the audio files. Thus, the behavior study is facilitated by choosing and accessing the corresponding index in the audio file. The complete indexing algorithm is processed on real data from the NUWC (Naval Undersea Warfare Center of the US Navy) and the AUTEC (Atlantic Undersea Test & Evaluation Center-Bahamas). Our model is validated by similar results from the US Navy (NUWC) and SOEST (School of Ocean and Earth Science and Technology) Hawaii university labs in a single whale case. Finally, as an illustration, we index a single whale sound file using the extracted whale's features provided by the tracking, and we present an example of an XML script structuring it.

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.

Semantic e-Science: From Microformats to Models

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Freemantle, J. R.; Aldridge, K. D.

2009-05-01

A platform has been developed to transform semi-structured ASCII data into a representation based on the eXtensible Markup Language (XML). A subsequent transformation allows the XML-based representation to be rendered in the Resource Description Format (RDF). Editorial metadata, expressed as external annotations (via XML Pointer Language), also survives this transformation process (e.g., Lumb et al., http://dx.doi.org/10.1016/j.cageo.2008.03.009). Because the XML-to-RDF transformation uses XSLT (eXtensible Stylesheet Language Transformations), semantic microformats ultimately encode the scientific data (Lumb & Aldridge, http://dx.doi.org/10.1109/HPCS.2006.26). In building the relationship-centric representation in RDF, a Semantic Model of the scientific data is extracted. The systematic enhancement in the expressivity and richness of the scientific data results in representations of knowledge that are readily understood and manipulated by intelligent software agents. Thus scientists are able to draw upon various resources within and beyond their discipline to use in their scientific applications. Since the resulting Semantic Models are independent conceptualizations of the science itself, the representation of scientific knowledge and interaction with the same can stimulate insight from different perspectives. Using the Global Geodynamics Project (GGP) for the purpose of illustration, the introduction of GGP microformats enable a Semantic Model for the GGP that can be semantically queried (e.g., via SPARQL, http://www.w3.org/TR/rdf-sparql-query). Although the present implementation uses the Open Source Redland RDF Libraries (http://librdf.org/), the approach is generalizable to other platforms and to projects other than the GGP (e.g., Baker et al., Informatics and the 2007-2008 Electronic Geophysical Year, Eos Trans. Am. Geophys. Un., 89(48), 485-486, 2008).

Lapin Data Interchange Among Database, Analysis and Display Programs Using XML-Based Text Files

NASA Technical Reports Server (NTRS)

2004-01-01

The purpose 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. See Engineering Analysis Using a Web-Based Protocol by J.D. Schoeffler and R.W. Claus, NASA TM-2002-211981, October 2002. 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).

Pulse oximeter based mobile biotelemetry application.

PubMed

Işik, Ali Hakan; Güler, Inan

2012-01-01

Quality and features of tele-homecare are improved by information and communication technologies. In this context, a pulse oximeter-based mobile biotelemetry application is developed. With this application, patients can measure own oxygen saturation and heart rate through Bluetooth pulse oximeter at home. Bluetooth virtual serial port protocol is used to send the test results from pulse oximeter to the smart phone. These data are converted into XML type and transmitted to remote web server database via smart phone. In transmission of data, GPRS, WLAN or 3G can be used. The rule based algorithm is used in the decision making process. By default, the threshold value of oxygen saturation is 80; the heart rate threshold values are 40 and 150 respectively. If the patient's heart rate is out of the threshold values or the oxygen saturation is below the threshold value, an emergency SMS is sent to the doctor. By this way, the directing of an ambulance to the patient can be performed by doctor. The doctor for different patients can change these threshold values. The conversion of the result of the evaluated data to SMS XML template is done on the web server. Another important component of the application is web-based monitoring of pulse oximeter data. The web page provides access to of all patient data, so the doctors can follow their patients and send e-mail related to the evaluation of the disease. In addition, patients can follow own data on this page. Eight patients have become part of the procedure. It is believed that developed application will facilitate pulse oximeter-based measurement from anywhere and at anytime.

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

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

NASA Astrophysics Data System (ADS)

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

2005-11-01

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

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

USGS Publications Warehouse

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

2005-01-01

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

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.

The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

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

Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan

2015-11-15

Purpose: Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. Methods: A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy ofmore » the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. Results: The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries.« less

The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery.

PubMed

Yu, Victoria Y; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A; Sheng, Ke

2015-11-01

Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy of the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries.

The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

PubMed Central

Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

2015-01-01

Purpose: Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. Methods: A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy of the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. Results: The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was attributed to phantom setup errors due to the slightly deformable and flexible phantom extremities. The estimated site-specific safety buffer distance with 0.001% probability of collision for (gantry-to-couch, gantry-to-phantom) was (1.23 cm, 3.35 cm), (1.01 cm, 3.99 cm), and (2.19 cm, 5.73 cm) for treatment to the head, lung, and prostate, respectively. Automated delivery to all three treatment sites was completed in 15 min and collision free using a digital Linac. Conclusions: An individualized collision prediction model for the purpose of noncoplanar beam delivery was developed and verified. With the model, the study has demonstrated the feasibility of predicting deliverable beams for an individual patient and then guiding fully automated noncoplanar treatment delivery. This work motivates development of clinical workflows and quality assurance procedures to allow more extensive use and automation of noncoplanar beam geometries. PMID:26520735

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

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...

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.

Automating Media Centers and Small Libraries: A Microcomputer-Based Approach.

ERIC Educational Resources Information Center

Meghabghab, Dania Bilal

Although the general automation process can be applied to most libraries, small libraries and media centers require a customized approach. Using a systematic approach, this guide covers each step and aspect of automation in a small library setting, and combines the principles of automation with field- tested activities. After discussing needs…

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.

Operational Based Vision Assessment Automated Vision Test Collection User Guide

DTIC Science & Technology

2017-05-15

repeatability to support correlation analysis. The AVT research grade tests also support interservice, international, industry, and academic partnerships...software, provides information concerning various menu options and operation of the test, and provides a brief description of each of the automated vision...2802, 6 Jun 2017. TABLE OF CONTENTS (concluded) Section Page 7.0 OBVA VISION TEST DESCRIPTIONS

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.

Decision Support Systems for Launch and Range Operations Using Jess

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar

2007-01-01

The virtual test bed for launch and range operations developed at NASA Ames Research Center consists of various independent expert systems advising on weather effects, toxic gas dispersions and human health risk assessment during space-flight operations. An individual dedicated server supports each expert system and the master system gather information from the dedicated servers to support the launch decision-making process. Since the test bed is based on the web system, reducing network traffic and optimizing the knowledge base is critical to its success of real-time or near real-time operations. Jess, a fast rule engine and powerful scripting environment developed at Sandia National Laboratory has been adopted to build the expert systems providing robustness and scalability. Jess also supports XML representation of knowledge base with forward and backward chaining inference mechanism. Facts added - to working memory during run-time operations facilitates analyses of multiple scenarios. Knowledge base can be distributed with one inference engine performing the inference process. This paper discusses details of the knowledge base and inference engine using Jess for a launch and range virtual test bed.

Automated Low-Cost Smartphone-Based Lateral Flow Saliva Test Reader for Drugs-of-Abuse Detection

PubMed Central

Carrio, Adrian; Sampedro, Carlos; Sanchez-Lopez, Jose Luis; Pimienta, Miguel; Campoy, Pascual

2015-01-01

Lateral flow assay tests are nowadays becoming powerful, low-cost diagnostic tools. Obtaining a result is usually subject to visual interpretation of colored areas on the test by a human operator, introducing subjectivity and the possibility of errors in the extraction of the results. While automated test readers providing a result-consistent solution are widely available, they usually lack portability. In this paper, we present a smartphone-based automated reader for drug-of-abuse lateral flow assay tests, consisting of an inexpensive light box and a smartphone device. Test images captured with the smartphone camera are processed in the device using computer vision and machine learning techniques to perform automatic extraction of the results. A deep validation of the system has been carried out showing the high accuracy of the system. The proposed approach, applicable to any line-based or color-based lateral flow test in the market, effectively reduces the manufacturing costs of the reader and makes it portable and massively available while providing accurate, reliable results. PMID:26610513

Efficient processing of MPEG-21 metadata in the binary domain

NASA Astrophysics Data System (ADS)

Timmerer, Christian; Frank, Thomas; Hellwagner, Hermann; Heuer, Jörg; Hutter, Andreas

2005-10-01

XML-based metadata is widely adopted across the different communities and plenty of commercial and open source tools for processing and transforming are available on the market. However, all of these tools have one thing in common: they operate on plain text encoded metadata which may become a burden in constrained and streaming environments, i.e., when metadata needs to be processed together with multimedia content on the fly. In this paper we present an efficient approach for transforming such kind of metadata which are encoded using MPEG's Binary Format for Metadata (BiM) without additional en-/decoding overheads, i.e., within the binary domain. Therefore, we have developed an event-based push parser for BiM encoded metadata which transforms the metadata by a limited set of processing instructions - based on traditional XML transformation techniques - operating on bit patterns instead of cost-intensive string comparisons.

Ground Processing of Data From the Mars Exploration Rovers

NASA Technical Reports Server (NTRS)

Wright, Jesse; Sturdevant, Kathryn; Noble, David

2006-01-01

A computer program implements the Earth side of the protocol that governs the transfer of data files generated by the Mars Exploration Rovers. It also provides tools for viewing data in these files and integrating data-product files into automated and manual processes. It reconstitutes files from telemetry data packets. Even if only one packet is received, metadata provide enough information to enable this program to identify and use partial data products. This software can generate commands to acknowledge received files and retransmit missed parts of files, or it can feed a manual process to make decisions about retransmission. The software uses an Extensible Markup Language (XML) data dictionary to provide a generic capability for displaying files of basic types, and uses external "plug-in" application programs to provide more sophisticated displays. This program makes data products available with very low latency, and can trigger automated actions when complete or partial products are received. The software is easy to install and use. The only system requirement for installing the software is a Java J2SE 1.4 platform. Several instances of the software can be executed simultaneously on the same machine.

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.

Monitoring the Performance of Human and Automated Scores for Spoken Responses

ERIC Educational Resources Information Center

Wang, Zhen; Zechner, Klaus; Sun, Yu

2018-01-01

As automated scoring systems for spoken responses are increasingly used in language assessments, testing organizations need to analyze their performance, as compared to human raters, across several dimensions, for example, on individual items or based on subgroups of test takers. In addition, there is a need in testing organizations to establish…

Enhanced Management of and Access to Hurricane Sandy Ocean and Coastal Mapping Data

NASA Astrophysics Data System (ADS)

Eakins, B.; Neufeld, D.; Varner, J. D.; McLean, S. J.

2014-12-01

NOAA's National Geophysical Data Center (NGDC) has significantly improved the discovery and delivery of its geophysical data holdings, initially targeting ocean and coastal mapping (OCM) data in the U.S. coastal region impacted by Hurricane Sandy in 2012. We have developed a browser-based, interactive interface that permits users to refine their initial map-driven data-type choices prior to bulk download (e.g., by selecting individual surveys), including the ability to choose ancillary files, such as reports or derived products. Initial OCM data types now available in a U.S. East Coast map viewer, as well as underlying web services, include: NOS hydrographic soundings and multibeam sonar bathymetry. Future releases will include trackline geophysics, airborne topographic and bathymetric-topographic lidar, bottom sample descriptions, and digital elevation models.This effort also includes working collaboratively with other NOAA offices and partners to develop automated methods to receive and verify data, stage data for archive, and notify data providers when ingest and archive are completed. We have also developed improved metadata tools to parse XML and auto-populate OCM data catalogs, support the web-based creation and editing of ISO-compliant metadata records, and register metadata in appropriate data portals. This effort supports a variety of NOAA mission requirements, from safe navigation to coastal flood forecasting and habitat characterization.

Automated spot defect characterization in a field portable night vision goggle test set

NASA Astrophysics Data System (ADS)

Scopatz, Stephen; Ozten, Metehan; Aubry, Gilles; Arquetoux, Guillaume

2018-05-01

This paper discusses a new capability developed for and results from a field portable test set for Gen 2 and Gen 3 Image Intensifier (I2) tube-based Night Vision Goggles (NVG). A previous paper described the test set and the automated and semi-automated tests supported for NVGs including a Knife Edge MTF test to replace the operator's interpretation of the USAF 1951 resolution chart. The major improvement and innovation detailed in this paper is the use of image analysis algorithms to automate the characterization of spot defects of I² tubes with the same test set hardware previously presented. The original and still common Spot Defect Test requires the operator to look through the NVGs at target of concentric rings; compare the size of the defects to a chart and manually enter the results into a table based on the size and location of each defect; this is tedious and subjective. The prior semi-automated improvement captures and displays an image of the defects and the rings; allowing the operator determine the defects with less eyestrain; while electronically storing the image and the resulting table. The advanced Automated Spot Defect Test utilizes machine vision algorithms to determine the size and location of the defects, generates the result table automatically and then records the image and the results in a computer-generated report easily usable for verification. This is inherently a more repeatable process that ensures consistent spot detection independent of the operator. Results of across several NVGs will be presented.

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.

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

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

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

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic.

Automated knowledge generation

NASA Technical Reports Server (NTRS)

Myler, Harley R.; Gonzalez, Avelino J.

1988-01-01

The general objectives of the NASA/UCF Automated Knowledge Generation Project were the development of an intelligent software system that could access CAD design data bases, interpret them, and generate a diagnostic knowledge base in the form of a system model. The initial area of concentration is in the diagnosis of the process control system using the Knowledge-based Autonomous Test Engineer (KATE) diagnostic system. A secondary objective was the study of general problems of automated knowledge generation. A prototype was developed, based on object-oriented language (Flavors).

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies.

PubMed

Surinova, Silvia; Hüttenhain, Ruth; Chang, Ching-Yun; Espona, Lucia; Vitek, Olga; Aebersold, Ruedi

2013-08-01

Targeted proteomics based on selected reaction monitoring (SRM) mass spectrometry is commonly used for accurate and reproducible quantification of protein analytes in complex biological mixtures. Strictly hypothesis-driven, SRM assays quantify each targeted protein by collecting measurements on its peptide fragment ions, called transitions. To achieve sensitive and accurate quantitative results, experimental design and data analysis must consistently account for the variability of the quantified transitions. This consistency is especially important in large experiments, which increasingly require profiling up to hundreds of proteins over hundreds of samples. Here we describe a robust and automated workflow for the analysis of large quantitative SRM data sets that integrates data processing, statistical protein identification and quantification, and dissemination of the results. The integrated workflow combines three software tools: mProphet for peptide identification via probabilistic scoring; SRMstats for protein significance analysis with linear mixed-effect models; and PASSEL, a public repository for storage, retrieval and query of SRM data. The input requirements for the protocol are files with SRM traces in mzXML format, and a file with a list of transitions in a text tab-separated format. The protocol is especially suited for data with heavy isotope-labeled peptide internal standards. We demonstrate the protocol on a clinical data set in which the abundances of 35 biomarker candidates were profiled in 83 blood plasma samples of subjects with ovarian cancer or benign ovarian tumors. The time frame to realize the protocol is 1-2 weeks, depending on the number of replicates used in the experiment.

Development of automated testing tools for traffic control signals and devices (NTCIP and Security) phase 2.

DOT National Transportation Integrated Search

2015-02-01

Through a coordinated effort among the electrical engineering research team of the Florida State : University (FSU) and key Florida Department of Transportation (FDOT) personnel, an NTCIP-based : automated testing system for NTCIP-compliant ASC has b...

Development of an automated asbestos counting software based on fluorescence microscopy.

PubMed

Alexandrov, Maxym; Ichida, Etsuko; Nishimura, Tomoki; Aoki, Kousuke; Ishida, Takenori; Hirota, Ryuichi; Ikeda, Takeshi; Kawasaki, Tetsuo; Kuroda, Akio

2015-01-01

An emerging alternative to the commonly used analytical methods for asbestos analysis is fluorescence microscopy (FM), which relies on highly specific asbestos-binding probes to distinguish asbestos from interfering non-asbestos fibers. However, all types of microscopic asbestos analysis require laborious examination of large number of fields of view and are prone to subjective errors and large variability between asbestos counts by different analysts and laboratories. A possible solution to these problems is automated counting of asbestos fibers by image analysis software, which would lower the cost and increase the reliability of asbestos testing. This study seeks to develop a fiber recognition and counting software for FM-based asbestos analysis. We discuss the main features of the developed software and the results of its testing. Software testing showed good correlation between automated and manual counts for the samples with medium and high fiber concentrations. At low fiber concentrations, the automated counts were less accurate, leading us to implement correction mode for automated counts. While the full automation of asbestos analysis would require further improvements in accuracy of fiber identification, the developed software could already assist professional asbestos analysts and record detailed fiber dimensions for the use in epidemiological research.

Development and evaluation of online evidence based guideline bank system.

PubMed

Park, Myonghwa

2006-01-01

The purpose of this study was to develop and evaluate the online evidence-based nursing practice guideline bank system to support the best evidence-based decision in the clinical and community practice settings. The main homepage consisted of seven modules for introduction of site, EBN, guideline bank, guideline development, guideline review, related sites, and community. The major contents in the guidelines were purpose, developer, intended audience, method of development, target population, testing, knowledge components, and evaluation. Electronic versions of the guidelines were displayed by XML, PDF, and PDA versions. The system usability were evaluated by general users, guideline developers, and guideline reviewers on the web and the results showed high scores of satisfaction. This online evidence-based guideline bank system could support nurses' best and cost-effective clinical decision using the sharable standardized guidelines with education module of evidence based nursing.

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

The efficacy of a Web-based counterargument tutor.

PubMed

Wolfe, Christopher R; Britt, M Anne; Petrovic, Melina; Albrecht, Michael; Kopp, Kristopher

2009-08-01

In two experiments, we developed and tested an interactive Web-based tutor to help students identify and evaluate counterarguments. In Experiment 1, we determined the extent to which high- and low-argumentationability participants were able to identify counterarguments. We tested the effectiveness of having participants read didactic text regarding counterarguments and highlight claims. Both preparations had some positive effects that were often limited to high-ability participants. The Web-based intervention included interactive exercises on identifying and using counterarguments. Web-based presentation was state driven, using a Java Server Pages page. As participants progressively identified argument elements, the page changed display state and presented feedback by checking what the user clicked against elements that we had coded in XML beforehand. Instructions and feedback strings were indexed by state, so that changing state selected new text to display. In Experiment 2, the tutor was effective in teaching participants to identify counterarguments, recognize responses, and determine whether counterarguments were rebutted, dismissed, or conceded.

TU-G-BRD-02: Automated Systematic Quality Assurance Program for Radiation Oncology Information System Upgrades

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

Zhang, B; Yi, B; Eley, J

Purpose: To: (1) describe an independent, automated, systematic software-based protocol for verifying clinical data accuracy/integrity for mitigation of data corruption/loss risks following radiation oncology information system (ROIS) upgrades; and (2) report on application of this approach in an academic/community practice environment. Methods: We propose a robust approach to perform quality assurance on the ROIS after an upgrade, targeting four data sources: (1) ROIS relational database; (2) ROIS DICOM interface; (3) ROIS treatment machine data configuration; and (4) ROIS-generated clinical reports. We investigated the database schema for differences between pre-/post-upgrade states. Paired DICOM data streams for the same object (such asmore » RT-Plan/Treatment Record) were compared between pre-/post-upgrade states for data corruption. We examined machine configuration and related commissioning data files for changes and corruption. ROIS-generated treatment appointment and treatment parameter reports were compared to ensure patient encounter and treatment plan accuracy. This protocol was supplemented by an end-to-end clinical workflow test to verify essential ROI functionality and integrity of components interfaced during patient care chain of activities. We describe the implementation of this protocol during a Varian ARIA system upgrade at our clinic. Results: We verified 1,638 data tables with 2.4 billion data records. For 222 under-treatment patients, 605 DICOM RT plans and 13,480 DICOM treatment records retrieved from the ROIS DICOM interface were compared, with no differences in fractions, doses delivered, or treatment parameters. We identified 82 new data tables and 78 amended/deleted tables consistent with the upgrade. Reports for 5,073 patient encounters over a 2-week horizon were compared and were identical to those before the upgrade. Content in 12,237 xml machine files was compared, with no differences identified. Conclusion: An independent QA/validation approach for ROIS upgrades was developed and implemented at our clinic. The success of this approach ensures a robust QA of ROIS upgrades without manual paper/electronic checks and associated intensive labor.« less

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

Automated Microwave Dielectric Constant Measurement

DTIC Science & Technology

1987-03-01

IJSWC TR 86-46 AD.-A 184 182 AUTOMATED MICROWAVE DIELECTRIC CONSTANT MEASUREMENT SYTIEM BY B. C. GLANCY A. KRALL PESEARCH AND TECHNOLOGY DEPARTMENT...NO0. NO. ACCESSION NO. Silver Spring, Maryland 20903-500061152N ZROO1 ZRO131 R1AA29 11. TITLE (Include Security Classification) AUTOMATED MICROWAVE ...constants as a funct on of microwave frequency has been simplified using an automated testing apparatus. This automated procedure is based on the use of a

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

PubMed

Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

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.

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience

PubMed Central

Vella, Michael; Cannon, Robert C.; Crook, Sharon; Davison, Andrew P.; Ganapathy, Gautham; Robinson, Hugh P. C.; Silver, R. Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. PMID:24795618

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.

Telemetry Attributes Transfer Standard (TMATS) Handbook

DTIC Science & Technology

2017-01-01

information regarding the project’s security classification guide and/or downgrading information should be provided as a comment. (G\\ COM ) G\\SC:U; The...96TH TEST WING 412TH TEST WING ARNOLD ENGINEERING DEVELOPMENT COMPLEX NATIONAL AERONAUTICS AND SPACE ADMINISTRATION This page intentionally...TMATS) Handbook, RCC Document 124-17, January 2017 v Figure 2-16. “Look and Feel” D-Group Engine Temperature Measurement Example XML

An object-oriented approach for harmonization of multimedia markup languages

NASA Astrophysics Data System (ADS)

Chen, Yih-Feng; Kuo, May-Chen; Sun, Xiaoming; Kuo, C.-C. Jay

2003-12-01

An object-oriented methodology is proposed to harmonize several different markup languages in this research. First, we adopt the Unified Modelling Language (UML) as the data model to formalize the concept and the process of the harmonization process between the eXtensible Markup Language (XML) applications. Then, we design the Harmonization eXtensible Markup Language (HXML) based on the data model and formalize the transformation between the Document Type Definitions (DTDs) of the original XML applications and HXML. The transformation between instances is also discussed. We use the harmonization of SMIL and X3D as an example to demonstrate the proposed methodology. This methodology can be generalized to various application domains.

Managing and Querying Image Annotation and Markup in XML.

PubMed

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

Managing and Querying Image Annotation and Markup in XML

PubMed Central

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

CMO: Cruise Metadata Organizer for JAMSTEC Research Cruises

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Space Communications Emulation Facility

NASA Technical Reports Server (NTRS)

Hill, Chante A.

2004-01-01

Establishing space communication between ground facilities and other satellites is a painstaking task that requires many precise calculations dealing with relay time, atmospheric conditions, and satellite positions, to name a few. The Space Communications Emulation Facility (SCEF) team here at NASA is developing a facility that will approximately emulate the conditions in space that impact space communication. The emulation facility is comprised of a 32 node distributed cluster of computers; each node representing a satellite or ground station. The objective of the satellites is to observe the topography of the Earth (water, vegetation, land, and ice) and relay this information back to the ground stations. Software originally designed by the University of Kansas, labeled the Emulation Manager, controls the interaction of the satellites and ground stations, as well as handling the recording of data. The Emulation Manager is installed on a Linux Operating System, employing both Java and C++ programming codes. The emulation scenarios are written in extensible Markup Language, XML. XML documents are designed to store, carry, and exchange data. With XML documents data can be exchanged between incompatible systems, which makes it ideal for this project because Linux, MAC and Windows Operating Systems are all used. Unfortunately, XML documents cannot display data like HTML documents. Therefore, the SCEF team uses XML Schema Definition (XSD) or just schema to describe the structure of an XML document. Schemas are very important because they have the capability to validate the correctness of data, define restrictions on data, define data formats, and convert data between different data types, among other things. At this time, in order for the Emulation Manager to open and run an XML emulation scenario file, the user must first establish a link between the schema file and the directory under which the XML scenario files are saved. This procedure takes place on the command line on the Linux Operating System. Once this link has been established the Emulation manager validates all the XML files in that directory against the schema file, before the actual scenario is run. Using some very sophisticated commercial software called the Satellite Tool Kit (STK) installed on the Linux box, the Emulation Manager is able to display the data and graphics generated by the execution of a XML emulation scenario file. The Emulation Manager software is written in JAVA programming code. Since the SCEF project is in the developmental stage, the source code for this type of software is being modified to better fit the requirements of the SCEF project. Some parameters for the emulation are hard coded, set at fixed values. Members of the SCEF team are altering the code to allow the user to choose the values of these hard coded parameters by inserting a toolbar onto the preexisting GUI.

The development of an automated flight test management system for flight test planning and monitoring

NASA Technical Reports Server (NTRS)

Hewett, Marle D.; Tartt, David M.; Duke, Eugene L.; Antoniewicz, Robert F.; Brumbaugh, Randal W.

1988-01-01

The development of an automated flight test management system (ATMS) as a component of a rapid-prototyping flight research facility for AI-based flight systems concepts is described. The rapid-prototyping facility includes real-time high-fidelity simulators, numeric and symbolic processors, and high-performance research aircraft modified to accept commands for a ground-based remotely augmented vehicle facility. The flight system configuration of the ATMS includes three computers: the TI explorer LX and two GOULD SEL 32/27s.

[Study on blood pressure standard in children using the automatic sphygmomanometer].

PubMed

Niida, Mami; Hataya, Hiroshi; Honda, Masataka

2015-01-01

In Japan, two treatment guidelines exist for pediatric patients with hypertension. The Guidelines for Drug Therapy in Pediatric Patients with Cardiovascular Diseases (JCS2012), by the Japanese Circulation Society, cite the stethoscopy-based American guidelines. The Guidelines for the Management of Hypertension (JSH2009), by the Japanese Society of Hypertension, focus on Japanese data obtained from automated sphygmomanometry. The frequent use of automated sphygmomanometers in clinical practice implies that the JSH2009 guidelines might be better; however with strict low reference values for the diastolic phase, overtreatment may result. Only the Japanese Circulation Society's guidelines include a therapeutic strategy, and the Chronic Kidney Disease (CKD) Guide, CKD Guidelines, and school urinary screening tests all cite these guidelines on stethoscopy-based blood pressure determination. Stethoscopy should be conducted during a medical examination; however, due to limited time in clinical practice, most physicians use automated sphygmomanometers while nevertheless relying on the Japanese Circulation Society reference values--which are stethoscopy-based. To find a compromise, we compared reference values in Japan with those from South Korea (automated sphygmomanometer-based) and those from the United States (stethoscopy-based). Moreover, we examined the results of recent accuracy tests for automated sphygmomanometers. Although the JSH2009 reference values for the systolic phase were consistent with those in the United States (stethoscopy-based), the reference values for the diastolic phase were lower. We observed the same tendency when comparing JSH2009 reference values with those in South Korea (automated sphygmomanometer-based). Conversely, there were only small differences between automated sphygmomanometry and mercury measurement, and we found it was possible to substitute the values from automated sphygmomanometry for stethoscopy. A large-scale study that takes into account patient height, measurement method, and treatment criteria is required to establish appropriate reference values. Even if automated sphygmomanometry is used until appropriate values are established, we consider the criteria provided in the American guidelines as appropriate.

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.

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.

Evaluation of a French medical multi-terminology indexer for the manual annotation of natural language medical reports of healthcare-associated infections.

PubMed

Sakji, Saoussen; Gicquel, Quentin; Pereira, Suzanne; Kergourlay, Ivan; Proux, Denys; Darmoni, Stéfan; Metzger, Marie-Hélène

2010-01-01

Surveillance of healthcare-associated infections is essential to prevention. A new collaborative project, namely ALADIN, was launched in January 2009 and aims to develop an automated detection tool based on natural language processing of medical documents. The objective of this study was to evaluate the annotation of natural language medical reports of healthcare-associated infections. A software MS Access application (NosIndex) has been developed to interface ECMT XML answer and manual annotation work. ECMT performances were evaluated by an infection control practitioner (ICP). Precision was evaluated for the 2 modules and recall only for the default module. Exclusion rate was defined as ratio between medical terms not found by ECMT and total number of terms evaluated. The medical discharge summaries were randomly selected in 4 medical wards. From the 247 medical terms evaluated, ECMT proposed 428 and 3,721 codes, respectively for the default and expansion modules. The precision was higher with the default module (P1=0.62) than with the expansion (P2=0.47). Performances of ECMT as support tool for the medical annotation were satisfactory.

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

77 FR 22707 - Electronic Reporting Under the Toxic Substances Control Act

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-17

... completes metadata information, the web-based tool validates the submission by performing a basic error... uploading PDF attachments or other file types, such as XML, and completing metadata information would be...

A compendium of controlled diffusion blades generated by an automated inverse design procedure

NASA Technical Reports Server (NTRS)

Sanz, Jose M.

1989-01-01

A set of sample cases was produced to test an automated design procedure developed at the NASA Lewis Research Center for the design of controlled diffusion blades. The range of application of the automated design procedure is documented. The results presented include characteristic compressor and turbine blade sections produced with the automated design code as well as various other airfoils produced with the base design method prior to the incorporation of the automated procedure.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*

PubMed Central

Medina-Aunon, J. Alberto; Martínez-Bartolomé, Salvador; López-García, Miguel A.; Salazar, Emilio; Navajas, Rosana; Jones, Andrew R.; Paradela, Alberto; Albar, Juan P.

2011-01-01

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. PMID:21983993

A comparison of adaptive and adaptable automation under different levels of environmental stress.

PubMed

Sauer, Juergen; Kao, Chung-Shan; Wastell, David

2012-01-01

The effectiveness of different forms of adaptive and adaptable automation was examined under low- and high-stress conditions, in the form of different levels of noise. Thirty-six participants were assigned to one of the three types of variable automation (adaptive event-based, adaptive performance-based and adaptable serving as a control condition). Participants received 3 h of training on a simulation of a highly automated process control task and were subsequently tested during a 4-h session under noise exposure and quiet conditions. The results for performance suggested no clear benefits of one automation control mode over the other two. However, it emerged that participants under adaptable automation adopted a more active system management strategy and reported higher levels of self-confidence than in the two adaptive control modes. Furthermore, the results showed higher levels of perceived workload, fatigue and anxiety for performance-based adaptive automation control than the other two modes. This study compared two forms of adaptive automation (where the automated system flexibly allocates tasks between human and machine) with adaptable automation (where the human allocates the tasks). The adaptable mode showed marginal advantages. This is of relevance, given that this automation mode may also be easier to design.

The use of an automated flight test management system in the development of a rapid-prototyping flight research facility

NASA Technical Reports Server (NTRS)

Duke, Eugene L.; Hewett, Marle D.; Brumbaugh, Randal W.; Tartt, David M.; Antoniewicz, Robert F.; Agarwal, Arvind K.

1988-01-01

An automated flight test management system (ATMS) and its use to develop a rapid-prototyping flight research facility for artificial intelligence (AI) based flight systems concepts are described. The ATMS provides a flight test engineer with a set of tools that assist in flight planning and simulation. This system will be capable of controlling an aircraft during the flight test by performing closed-loop guidance functions, range management, and maneuver-quality monitoring. The rapid-prototyping flight research facility is being developed at the Dryden Flight Research Facility of the NASA Ames Research Center (Ames-Dryden) to provide early flight assessment of emerging AI technology. The facility is being developed as one element of the aircraft automation program which focuses on the qualification and validation of embedded real-time AI-based systems.

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.

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).

Generating Test Templates via Automated Theorem Proving

NASA Technical Reports Server (NTRS)

Kancherla, Mani Prasad

1997-01-01

Testing can be used during the software development process to maintain fidelity between evolving specifications, program designs, and code implementations. We use a form of specification-based testing that employs the use of an automated theorem prover to generate test templates. A similar approach was developed using a model checker on state-intensive systems. This method applies to systems with functional rather than state-based behaviors. This approach allows for the use of incomplete specifications to aid in generation of tests for potential failure cases. We illustrate the technique on the cannonical triangle testing problem and discuss its use on analysis of a spacecraft scheduling system.

Proof-of-concept automation of propellant processing

NASA Technical Reports Server (NTRS)

Ramohalli, Kumar; Schallhorn, P. A.

1989-01-01

For space-based propellant production, automation of the process is needed. Currently, all phases of terrestrial production have some form of human interaction. A mixer was acquired to help perform the tasks of automation. A heating system to be used with the mixer was designed, built, and installed. Tests performed on the heating system verify design criteria. An IBM PS/2 personal computer was acquired for the future automation work. It is hoped that some the mixing process itself will be automated. This is a concept demonstration task; proving that propellant production can be automated reliably.

Universal Verification Methodology Based Register Test Automation Flow.

PubMed

Woo, Jae Hun; Cho, Yong Kwan; Park, Sun Kyu

2016-05-01

In today's SoC design, the number of registers has been increased along with complexity of hardware blocks. Register validation is a time-consuming and error-pron task. Therefore, we need an efficient way to perform verification with less effort in shorter time. In this work, we suggest register test automation flow based UVM (Universal Verification Methodology). UVM provides a standard methodology, called a register model, to facilitate stimulus generation and functional checking of registers. However, it is not easy for designers to create register models for their functional blocks or integrate models in test-bench environment because it requires knowledge of SystemVerilog and UVM libraries. For the creation of register models, many commercial tools support a register model generation from register specification described in IP-XACT, but it is time-consuming to describe register specification in IP-XACT format. For easy creation of register model, we propose spreadsheet-based register template which is translated to IP-XACT description, from which register models can be easily generated using commercial tools. On the other hand, we also automate all the steps involved integrating test-bench and generating test-cases, so that designers may use register model without detailed knowledge of UVM or SystemVerilog. This automation flow involves generating and connecting test-bench components (e.g., driver, checker, bus adaptor, etc.) and writing test sequence for each type of register test-case. With the proposed flow, designers can save considerable amount of time to verify functionality of registers.

China’s ASAT Test: Motivations and Implications

DTIC Science & Technology

2007-01-01

h i l l i P c . S a u n D e r S and c h a r l e S D . l u t e S Dr. Phillip C. saunders and Colonel Charles D. Lutes, UsaF, are senior Research...at <www.aviationweek.com/aw/generic/story_generic. jsp?channel= awst &id=news/aw012207p2.xml>. 11 Chris Buckley, “China confirms satellite test, says

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.

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.

Demonstrating NaradaBrokering as a Middleware Fabric for Grid-based Remote Visualization Services

NASA Astrophysics Data System (ADS)

Pallickara, S.; Erlebacher, G.; Yuen, D.; Fox, G.; Pierce, M.

2003-12-01

Remote Visualization Services (RVS) have tended to rely on approaches based on the client server paradigm. Here we demonstrate our approach - based on a distributed brokering infrastructure, NaradaBrokering [1] - that relies on distributed, asynchronous and loosely coupled interactions to meet the requirements and constraints of RVS. In our approach to RVS, services advertise their capabilities to the broker network that manages these service advertisements. Among the services considered within our system are those that perform graphic transformations, mediate access to specialized datasets and finally those that manage the execution of specified tasks. There could be multiple instances of each of these services and the system ensures that load for a given service is distributed efficiently over these service instances. We will demonstrate implementation of concepts that we outlined in the oral presentation. This would involve two or more visualization servers interacting asynchronously with multiple clients through NaradaBrokering. The communicating entities may exchange SOAP [2] (Simple Object Access Protocol) messages. SOAP is a lightweight protocol for exchange of information in a decentralized, distributed environment. It is an XML based protocol that consists of three parts: an envelope that describes what is in a message and how to process it, rules for expressing instances of application-defined data types, and a convention for representing remote invocation related operations. Furthermore, we will also demonstrate how clients can retrieve their results after prolonged disconnects or after any failures that might have taken place. The entities, services and clients alike, are not limited by the geographical distances that separate them. We are planning to test this system in the context of trans-Atlantic links separating interacting entities. {[1]} The NaradaBrokering Project: http://www.naradabrokering.org {[2]} Newcomer, E., 2002, Understanding web services: XML, WSDL, SOAP, and UDDI, Addison Wesley Professional.

QuakeML: Status of the XML-based Seismological Data Exchange Format

NASA Astrophysics Data System (ADS)

Euchner, Fabian; Schorlemmer, Danijel; Kästli, Philipp; Quakeml Working Group

2010-05-01

QuakeML is an XML-based data exchange standard for seismology that is in its fourth year of active community-driven development. The current release (version 1.2) is based on a public Request for Comments process that included contributions from ETH, GFZ, USC, SCEC, USGS, IRIS DMC, EMSC, ORFEUS, GNS, ZAMG, BRGM, Nanometrics, and ISTI. QuakeML has mainly been funded through the EC FP6 infrastructure project NERIES, in which it was endorsed as the preferred data exchange format. Currently, QuakeML services are being installed at several institutions around the globe, including EMSC, ORFEUS, ETH, Geoazur (Europe), NEIC, ANSS, SCEC/SCSN (USA), and GNS Science (New Zealand). Some of these institutions already provide QuakeML earthquake catalog web services. Several implementations of the QuakeML data model have been made. QuakePy, an open-source Python-based seismicity analysis toolkit using the QuakeML data model, is being developed at ETH. QuakePy is part of the software stack used in the Collaboratory for the Study of Earthquake Predictability (CSEP) testing center installations, developed by SCEC. Furthermore, the QuakeML data model is part of the SeisComP3 package from GFZ Potsdam. QuakeML is designed as an umbrella schema under which several sub-packages are collected. The present scope of QuakeML 1.2 covers a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Work on additional packages (macroseismic information, seismic inventory, and resource metadata) has been started, but is at an early stage. Contributions from the community that help to widen the thematic coverage of QuakeML are highly welcome. Online resources: http://www.quakeml.org, http://www.quakepy.org

PDS4: Harnessing the Power of Generate and Apache Velocity

NASA Astrophysics Data System (ADS)

Padams, J.; Cayanan, M.; Hardman, S.

2018-04-01

The PDS4 Generate Tool is a Java-based command-line tool developed by the Cartography and Imaging Sciences Nodes (PDSIMG) for generating PDS4 XML labels, from Apache Velocity templates and input metadata.

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.

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: ...

Automated quality control in a file-based broadcasting workflow

NASA Astrophysics Data System (ADS)

Zhang, Lina

2014-04-01

Benefit from the development of information and internet technologies, television broadcasting is transforming from inefficient tape-based production and distribution to integrated file-based workflows. However, no matter how many changes have took place, successful broadcasting still depends on the ability to deliver a consistent high quality signal to the audiences. After the transition from tape to file, traditional methods of manual quality control (QC) become inadequate, subjective, and inefficient. Based on China Central Television's full file-based workflow in the new site, this paper introduces an automated quality control test system for accurate detection of hidden troubles in media contents. It discusses the system framework and workflow control when the automated QC is added. It puts forward a QC criterion and brings forth a QC software followed this criterion. It also does some experiments on QC speed by adopting parallel processing and distributed computing. The performance of the test system shows that the adoption of automated QC can make the production effective and efficient, and help the station to achieve a competitive advantage in the media market.

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

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.

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.

Automated flight test management system

NASA Technical Reports Server (NTRS)

Hewett, M. D.; Tartt, D. M.; Agarwal, A.

1991-01-01

The Phase 1 development of an automated flight test management system (ATMS) as a component of a rapid prototyping flight research facility for artificial intelligence (AI) based flight concepts is discussed. The ATMS provides a flight engineer with a set of tools that assist in flight test planning, monitoring, and simulation. The system is also capable of controlling an aircraft during flight test by performing closed loop guidance functions, range management, and maneuver-quality monitoring. The ATMS is being used as a prototypical system to develop a flight research facility for AI based flight systems concepts at NASA Ames Dryden.

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

[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.

Enhancing SCORM Metadata for Assessment Authoring in E-Learning

ERIC Educational Resources Information Center

Chang, Wen-Chih; Hsu, Hui-Huang; Smith, Timothy K.; Wang, Chun-Chia

2004-01-01

With the rapid development of distance learning and the XML technology, metadata play an important role in e-Learning. Nowadays, many distance learning standards, such as SCORM, AICC CMI, IEEE LTSC LOM and IMS, use metadata to tag learning materials. However, most metadata models are used to define learning materials and test problems. Few…

Networking observers and observatories with remote telescope markup language

NASA Astrophysics Data System (ADS)

Hessman, Frederic V.; Tuparev, Georg; Allan, Alasdair

2006-06-01

Remote Telescope Markup Language (RTML) is an XML-based protocol for the transport of the high-level description of a set of observations to be carried out on a remote, robotic or service telescope. We describe how RTML is being used in a wide variety of contexts: the transport of service and robotic observing requests in the Hands-On Universe TM, ACP, eSTAR, and MONET networks; how RTML is easily combined with other XML protocols for more localized control of telescopes; RTML as a secondary observation report format for the IVOA's VOEvent protocol; the input format for a general-purpose observation simulator; and the observatory-independent means for carrying out request transactions for the international Heterogeneous Telescope Network (HTN).

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.

Model-Based Diagnosis in a Power Distribution Test-Bed

NASA Technical Reports Server (NTRS)

Scarl, E.; McCall, K.

1998-01-01

The Rodon model-based diagnosis shell was applied to a breadboard test-bed, modeling an automated power distribution system. The constraint-based modeling paradigm and diagnostic algorithm were found to adequately represent the selected set of test scenarios.

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.

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.

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.

Automated workflows for modelling chemical fate, kinetics and toxicity.

PubMed

Sala Benito, J V; Paini, Alicia; Richarz, Andrea-Nicole; Meinl, Thorsten; Berthold, Michael R; Cronin, Mark T D; Worth, Andrew P

2017-12-01

Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA). These biologically-based models will be coupled with chemistry-based prediction models that also automate the generation of key input parameters such as physicochemical properties. The development of automated software tools is an important step in harmonising and expediting the chemical safety assessment process. In this study, we illustrate how the KNIME Analytics Platform can be used to provide a user-friendly graphical interface for these biokinetic models, such as PBK models and VCBA, which simulates the fate of chemicals in vivo within the body and in vitro test systems respectively. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evaluation of an automated microplate technique in the Galileo system for ABO and Rh(D) blood grouping.

PubMed

Xu, Weiyi; Wan, Feng; Lou, Yufeng; Jin, Jiali; Mao, Weilin

2014-01-01

A number of automated devices for pretransfusion testing have recently become available. This study evaluated the Immucor Galileo System, a fully automated device based on the microplate hemagglutination technique for ABO/Rh (D) determinations. Routine ABO/Rh typing tests were performed on 13,045 samples using the Immucor automated instruments. Manual tube method was used to resolve ABO forward and reverse grouping discrepancies. D-negative test results were investigated and confirmed manually by the indirect antiglobulin test (IAT). The system rejected 70 tests for sample inadequacy. 87 samples were read as "No-type-determined" due to forward and reverse grouping discrepancies. 25 tests gave these results because of sample hemolysis. After further tests, we found 34 tests were caused by weakened RBC antibodies, 5 tests were attributable to weak A and/or B antigens, 4 tests were due to mixed-field reactions, and 8 tests had high titer cold agglutinin with blood qualifications which react only at temperatures below 34 degrees C. In the remaining 11 cases, irregular RBC antibodies were identified in 9 samples (seven anti-M and two anti-P) and two subgroups were identified in 2 samples (one A1 and one A2) by a reference laboratory. As for D typing, 2 weak D+ samples missed by automated systems gave negative results, but weak-positive reactions were observed in the IAT. The Immucor Galileo System is reliable and suited for ABO and D blood groups, some reasons may cause a discrepancy in ABO/D typing using a fully automated system. It is suggested that standardization of sample collection may improve the performance of the fully automated system.

Bluetooth Low Energy Peripheral Android Health App for Educational and Interoperability Testing Purposes.

PubMed

Frohner, Matthias; Urbauer, Philipp; Sauermann, Stefan

2017-01-01

Based on recent telemonitoring activities in Austria for enabling integrated health care, the communication interfaces between personal health devices (e.g. blood pressure monitor) and personal health gateway devices (e.g. smartphone, routing received information to wide area networks) play an important role. In order to ease testing of the Bluetooth Low Energy interface functionality of the personal health gateway devices, a personal health device simulator was developed. Based on specifications from the Bluetooth SIG a XML software test configuration file structure is defined that declares the specific features of the personal health devices simulated. Using this configuration file, different scenarios are defined, e.g. send a single measurement result from a blood pressure reading or sending multiple (historic) weight scale readings. The simulator is intended to be used for educational purposes in lectures, where the number of physical personal health devices can be reduced and learning can be improved. It could be shown that this simulator assists the development process of mHealth applications by reducing the time needed for development and testing.

Effects of Selected Task Performance Criteria at Initiating Adaptive Task Real locations

NASA Technical Reports Server (NTRS)

Montgomery, Demaris A.

2001-01-01

In the current report various performance assessment methods used to initiate mode transfers between manual control and automation for adaptive task reallocation were tested. Participants monitored two secondary tasks for critical events while actively controlling a process in a fictional system. One of the secondary monitoring tasks could be automated whenever operators' performance was below acceptable levels. Automation of the secondary task and transfer of the secondary task back to manual control were either human- or machine-initiated. Human-initiated transfers were based on the operator's assessment of the current task demands while machine-initiated transfers were based on the operators' performance. Different performance assessment methods were tested in two separate experiments.

Improving communication among nurses and patients.

PubMed

Unluturk, Mehmet S; Ozcanhan, Mehmet H; Dalkilic, Gokhan

2015-07-01

Patients use nurse call systems to signal nurses for medical help. Traditional push button-flashing lamp call systems are not integrated with other hospital automation systems. Therefore, nurse response time becomes a matter of personal discretion. The improvement obtained by integrating a pager system into the nurse call systems does not increase care efficiency, because unnecessary visits are still not eliminated. To obtain an immediate response and a purposeful visit by a nurse; regardless of the location of nurse in hospital, traditional systems have to be improved by intelligent telephone system integration. The results of the developed Nurse Call System Software (NCSS), the Wireless Phone System Software (WPSS), the Location System Software (LSS) and the communication protocol are provided, together with detailed XML message structures. The benefits of the proposed system are also discussed and the direction of future work is presented. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

DendroPy: a Python library for phylogenetic computing.

PubMed

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

QRev—Software for computation and quality assurance of acoustic doppler current profiler moving-boat streamflow measurements—Technical manual for version 2.8

USGS Publications Warehouse

Mueller, David S.

2016-06-21

The software program, QRev applies common and consistent computational algorithms combined with automated filtering and quality assessment of the data to improve the quality and efficiency of streamflow measurements and helps ensure that U.S. Geological Survey streamflow measurements are consistent, accurate, and independent of the manufacturer of the instrument used to make the measurement. Software from different manufacturers uses different algorithms for various aspects of the data processing and discharge computation. The algorithms used by QRev to filter data, interpolate data, and compute discharge are documented and compared to the algorithms used in the manufacturers’ software. QRev applies consistent algorithms and creates a data structure that is independent of the data source. QRev saves an extensible markup language (XML) file that can be imported into databases or electronic field notes software. This report is the technical manual for version 2.8 of QRev.

A Validity-Based Approach to Quality Control and Assurance of Automated Scoring

ERIC Educational Resources Information Center

Bejar, Isaac I.

2011-01-01

Automated scoring of constructed responses is already operational in several testing programmes. However, as the methodology matures and the demand for the utilisation of constructed responses increases, the volume of automated scoring is likely to increase at a fast pace. Quality assurance and control of the scoring process will likely be more…

Applications of Automation Methods for Nonlinear Fracture Test Analysis

NASA Technical Reports Server (NTRS)

Allen, Phillip A.; Wells, Douglas N.

2013-01-01

As fracture mechanics material testing evolves, the governing test standards continue to be refined to better reflect the latest understanding of the physics of the fracture processes involved. The traditional format of ASTM fracture testing standards, utilizing equations expressed directly in the text of the standard to assess the experimental result, is self-limiting in the complexity that can be reasonably captured. The use of automated analysis techniques to draw upon a rich, detailed solution database for assessing fracture mechanics tests provides a foundation for a new approach to testing standards that enables routine users to obtain highly reliable assessments of tests involving complex, non-linear fracture behavior. Herein, the case for automating the analysis of tests of surface cracks in tension in the elastic-plastic regime is utilized as an example of how such a database can be generated and implemented for use in the ASTM standards framework. The presented approach forms a bridge between the equation-based fracture testing standards of today and the next generation of standards solving complex problems through analysis automation.

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.

Program Management Tool

NASA Technical Reports Server (NTRS)

Gawadiak, Yuri; Wong, Alan; Maluf, David; Bell, David; Gurram, Mohana; Tran, Khai Peter; Hsu, Jennifer; Yagi, Kenji; Patel, Hemil

2007-01-01

The Program Management Tool (PMT) is a comprehensive, Web-enabled business intelligence software tool for assisting program and project managers within NASA enterprises in gathering, comprehending, and disseminating information on the progress of their programs and projects. The PMT provides planning and management support for implementing NASA programmatic and project management processes and requirements. It provides an online environment for program and line management to develop, communicate, and manage their programs, projects, and tasks in a comprehensive tool suite. The information managed by use of the PMT can include monthly reports as well as data on goals, deliverables, milestones, business processes, personnel, task plans, monthly reports, and budgetary allocations. The PMT provides an intuitive and enhanced Web interface to automate the tedious process of gathering and sharing monthly progress reports, task plans, financial data, and other information on project resources based on technical, schedule, budget, and management criteria and merits. The PMT is consistent with the latest Web standards and software practices, including the use of Extensible Markup Language (XML) for exchanging data and the WebDAV (Web Distributed Authoring and Versioning) protocol for collaborative management of documents. The PMT provides graphical displays of resource allocations in the form of bar and pie charts using Microsoft Excel Visual Basic for Application (VBA) libraries. The PMT has an extensible architecture that enables integration of PMT with other strategic-information software systems, including, for example, the Erasmus reporting system, now part of the NASA Integrated Enterprise Management Program (IEMP) tool suite, at NASA Marshall Space Flight Center (MSFC). The PMT data architecture provides automated and extensive software interfaces and reports to various strategic information systems to eliminate duplicative human entries and minimize data integrity issues among various NASA systems that impact schedules and planning.

Students' Perceived Usefulness of Formative Feedback for a Computer-Adaptive Test

ERIC Educational Resources Information Center

Lilley, Mariana; Barker, Trevor

2007-01-01

In this paper we report on research related to the provision of automated feedback based on a computer adaptive test (CAT), used in formative assessment. A cohort of 76 second year university undergraduates took part in a formative assessment with a CAT and were provided with automated feedback on their performance. A sample of students responded…

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.

Training Materials and Data Requirements for Unit Conduct of Fire Trainer (U-COFT) Training Test Support Plan

DTIC Science & Technology

1980-08-01

DESIGN GROUP I GROUP II GROUP III (XMl Tank) (Chrysler UCOFT) (GE UCOFT) Pretest ...training plan design are that: 1. Tank Commanders and Gunners will have been transition trained on the "MI prior to assign- mint to a test group . Cuirrent...posttests on the XMI for each group . Also, Loaders and Drivers are required for the Group I device pretest , gunnery portion of the

Improved maintainability of space-based reusable rocket engines

NASA Technical Reports Server (NTRS)

Barkhoudarian, S.; Szemenyei, B.; Nelson, R. S.; Pauckert, R.; Harmon, T.

1988-01-01

Advanced, noninferential, noncontacting, in situ measurement technologies, combined with automated testing and expert systems, can provide continuous, automated health monitoring of critical space-based rocket engine components, requiring minimal disassembly and no manual data analysis, thus enhancing their maintainability. This paper concentrates on recent progress of noncontacting combustion chamber wall thickness condition-monitoring technologies.

Enhancing Ear and Hearing Health Access for Children With Technology and Connectivity.

PubMed

Swanepoel, De Wet

2017-10-12

Technology and connectivity advances are demonstrating increasing potential to improve access of service delivery to persons with hearing loss. This article demonstrates use cases from community-based hearing screening and automated diagnosis of ear disease. This brief report reviews recent evidence for school- and home-based hearing testing in underserved communities using smartphone technologies paired with calibrated headphones. Another area of potential impact facilitated by technology and connectivity is the use of feature extraction algorithms to facilitate automated diagnosis of most common ear conditions from video-otoscopic images. Smartphone hearing screening using calibrated headphones demonstrated equivalent sensitivity and specificity for school-based hearing screening. Automating test sequences with a forced-choice response paradigm allowed persons with minimal training to offer screening in underserved communities. The automated image analysis and diagnosis system for ear disease demonstrated an overall accuracy of 80.6%, which is up to par and exceeds accuracy rates previously reported for general practitioners and pediatricians. The emergence of these tools that capitalize on technology and connectivity advances enables affordable and accessible models of service delivery for community-based ear and hearing care.

3D web based learning of medical equipment employed in intensive care units.

PubMed

Cetin, Aydın

2012-02-01

In this paper, both synchronous and asynchronous web based learning of 3D medical equipment models used in hospital intensive care unit have been described over the moodle course management system. 3D medical equipment models were designed with 3ds Max 2008, then converted to ASE format and added interactivity displayed with Viewpoint-Enliven. 3D models embedded in a web page in html format with dynamic interactivity-rotating, panning and zooming by dragging a mouse over images-and descriptive information is embedded to 3D model by using xml format. A pilot test course having 15 h was applied to technicians who is responsible for intensive care unit at Medical Devices Repairing and Maintenance Center (TABOM) of Turkish High Specialized Hospital.

[Design and Implementation of a Mobile Operating Room Information Management System Based on Electronic Medical Record].

PubMed

Liu, Baozhen; Liu, Zhiguo; Wang, Xianwen

2015-06-01

A mobile operating room information management system with electronic medical record (EMR) is designed to improve work efficiency and to enhance the patient information sharing. In the operating room, this system acquires the information from various medical devices through the Client/Server (C/S) pattern, and automatically generates XML-based EMR. Outside the operating room, this system provides information access service by using the Browser/Server (B/S) pattern. Software test shows that this system can correctly collect medical information from equipment and clearly display the real-time waveform. By achieving surgery records with higher quality and sharing the information among mobile medical units, this system can effectively reduce doctors' workload and promote the information construction of the field hospital.

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

Objective The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. Materials and Methods ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Results Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. Discussion The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. Conclusion A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic. PMID:23019241

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.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

PubMed

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; Del-Toro, Noemi; Dianes, Jose A; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets*

PubMed Central

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; del-Toro, Noemi; Dianes, Jose A.; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE. The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. PMID:26545397

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.

The NOAA IOOS Data Integration Framework: Initial Implementation Report

DTIC Science & Technology

2008-09-01

based services (http://www.opengeospatial.org/); NOAA is a Principal Member. Figure 2: Specialization of XML for in situ data To standardize...1 OGC is a non-profit, international, voluntary consensus organization that develops standards for geospatial and location

78 FR 66039 - Modification of National Customs Automation Program Test Concerning Automated Commercial...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-04

... Customs Automation Program Test Concerning Automated Commercial Environment (ACE) Cargo Release (Formerly... Simplified Entry functionality in the Automated Commercial Environment (ACE). Originally, the test was known...) test concerning Automated Commercial Environment (ACE) Simplified Entry (SE test) functionality is...

Design and test of an automated version of the modified Jebsen test of hand function using Microsoft Kinect.

PubMed

Simonsen, Daniel; Nielsen, Ida F; Spaich, Erika G; Andersen, Ole K

2017-05-02

The present paper describes the design and evaluation of an automated version of the Modified Jebsen Test of Hand Function (MJT) based on the Microsoft Kinect sensor. The MJT was administered twice to 11 chronic stroke subjects with varying degrees of hand function deficits. The test times of the MJT were evaluated manually by a therapist using a stopwatch, and automatically using the Microsoft Kinect sensor. The ground truth times were assessed based on inspection of the video-recordings. The agreement between the methods was evaluated along with the test-retest performance. The results from Bland-Altman analysis showed better agreement between the ground truth times and the automatic MJT time evaluations compared to the agreement between the ground truth times and the times estimated by the therapist. The results from the test-retest performance showed that the subjects significantly improved their performance in several subtests of the MJT, indicating a practice effect. The results from the test showed that the Kinect can be used for automating the MJT.

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

Rapid toxicity detection in water quality control utilizing automated multispecies biomonitoring for permanent space stations

NASA Technical Reports Server (NTRS)

Morgan, E. L.; Young, R. C.; Smith, M. D.; Eagleson, K. W.

1986-01-01

The objective of this study was to evaluate proposed design characteristics and applications of automated biomonitoring devices for real-time toxicity detection in water quality control on-board permanent space stations. Simulated tests in downlinking transmissions of automated biomonitoring data to Earth-receiving stations were simulated using satellite data transmissions from remote Earth-based stations.

Two Automated Techniques for Carotid Lumen Diameter Measurement: Regional versus Boundary Approaches.

PubMed

Araki, Tadashi; Kumar, P Krishna; Suri, Harman S; Ikeda, Nobutaka; Gupta, Ajay; Saba, Luca; Rajan, Jeny; Lavra, Francesco; Sharma, Aditya M; Shafique, Shoaib; Nicolaides, Andrew; Laird, John R; Suri, Jasjit S

2016-07-01

The degree of stenosis in the carotid artery can be predicted using automated carotid lumen diameter (LD) measured from B-mode ultrasound images. Systolic velocity-based methods for measurement of LD are subjective. With the advancement of high resolution imaging, image-based methods have started to emerge. However, they require robust image analysis for accurate LD measurement. This paper presents two different algorithms for automated segmentation of the lumen borders in carotid ultrasound images. Both algorithms are modeled as a two stage process. Stage one consists of a global-based model using scale-space framework for the extraction of the region of interest. This stage is common to both algorithms. Stage two is modeled using a local-based strategy that extracts the lumen interfaces. At this stage, the algorithm-1 is modeled as a region-based strategy using a classification framework, whereas the algorithm-2 is modeled as a boundary-based approach that uses the level set framework. Two sets of databases (DB), Japan DB (JDB) (202 patients, 404 images) and Hong Kong DB (HKDB) (50 patients, 300 images) were used in this study. Two trained neuroradiologists performed manual LD tracings. The mean automated LD measured was 6.35 ± 0.95 mm for JDB and 6.20 ± 1.35 mm for HKDB. The precision-of-merit was: 97.4 % and 98.0 % w.r.t to two manual tracings for JDB and 99.7 % and 97.9 % w.r.t to two manual tracings for HKDB. Statistical tests such as ANOVA, Chi-Squared, T-test, and Mann-Whitney test were conducted to show the stability and reliability of the automated techniques.

VERAIn

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

Simunovic, Srdjan

2015-02-16

CASL's modeling and simulation technology, the Virtual Environment for Reactor Applications (VERA), incorporates coupled physics and science-based models, state-of-the-art numerical methods, modern computational science, integrated uncertainty quantification (UQ) and validation against data from operating pressurized water reactors (PWRs), single-effect experiments, and integral tests. The computational simulation component of VERA is the VERA Core Simulator (VERA-CS). The core simulator is the specific collection of multi-physics computer codes used to model and deplete a LWR core over multiple cycles. The core simulator has a single common input file that drives all of the different physics codes. The parser code, VERAIn, converts VERAmore » Input into an XML file that is used as input to different VERA codes.« less

A knowledge-based approach to automated planning for hepatocellular carcinoma.

PubMed

Zhang, Yujie; Li, Tingting; Xiao, Han; Ji, Weixing; Guo, Ming; Zeng, Zhaochong; Zhang, Jianying

2018-01-01

To build a knowledge-based model of liver cancer for Auto-Planning, a function in Pinnacle, which is used as an automated inverse intensity modulated radiation therapy (IMRT) planning system. Fifty Tomotherapy patients were enrolled to extract the dose-volume histograms (DVHs) information and construct the protocol for Auto-Planning model. Twenty more patients were chosen additionally to test the model. Manual planning and automatic planning were performed blindly for all twenty test patients with the same machine and treatment planning system. The dose distributions of target and organs at risks (OARs), along with the working time for planning, were evaluated. Statistically significant results showed that automated plans performed better in target conformity index (CI) while mean target dose was 0.5 Gy higher than manual plans. The differences between target homogeneity indexes (HI) of the two methods were not statistically significant. Additionally, the doses of normal liver, left kidney, and small bowel were significantly reduced with automated plan. Particularly, mean dose and V15 of normal liver were 1.4 Gy and 40.5 cc lower with automated plans respectively. Mean doses of left kidney and small bowel were reduced with automated plans by 1.2 Gy and 2.1 Gy respectively. In contrast, working time was also significantly reduced with automated planning. Auto-Planning shows availability and effectiveness in our knowledge-based model for liver cancer. © 2017 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Automated Test Requirement Document Generation

DTIC Science & Technology

1987-11-01

DIAGNOSTICS BASED ON THE PRINCIPLES OF ARTIFICIAL INTELIGENCE ", 1984 International Test Conference, 01Oct84, (A3, 3, Cs D3, E2, G2, H2, 13, J6, K) 425...j0O GLOSSARY OF ACRONYMS 0 ABBREVIATION DEFINITION AFSATCOM Air Force Satellite Communication Al Artificial Intelligence ASIC Application Specific...In-Test Equipment (BITE) and AI ( Artificial Intelligence) - Expert Systems - need to be fully applied before a completely automated process can be

Dealing with Diversity in Computational Cancer Modeling

PubMed Central

Johnson, David; McKeever, Steve; Stamatakos, Georgios; Dionysiou, Dimitra; Graf, Norbert; Sakkalis, Vangelis; Marias, Konstantinos; Wang, Zhihui; Deisboeck, Thomas S.

2013-01-01

This paper discusses the need for interconnecting computational cancer models from different sources and scales within clinically relevant scenarios to increase the accuracy of the models and speed up their clinical adaptation, validation, and eventual translation. We briefly review current interoperability efforts drawing upon our experiences with the development of in silico models for predictive oncology within a number of European Commission Virtual Physiological Human initiative projects on cancer. A clinically relevant scenario, addressing brain tumor modeling that illustrates the need for coupling models from different sources and levels of complexity, is described. General approaches to enabling interoperability using XML-based markup languages for biological modeling are reviewed, concluding with a discussion on efforts towards developing cancer-specific XML markup to couple multiple component models for predictive in silico oncology. PMID:23700360

Continuous stacking computational approach based automated microscope slide scanner

NASA Astrophysics Data System (ADS)

Murali, Swetha; Adhikari, Jayesh Vasudeva; Jagannadh, Veerendra Kalyan; Gorthi, Sai Siva

2018-02-01

Cost-effective and automated acquisition of whole slide images is a bottleneck for wide-scale deployment of digital pathology. In this article, a computation augmented approach for the development of an automated microscope slide scanner is presented. The realization of a prototype device built using inexpensive off-the-shelf optical components and motors is detailed. The applicability of the developed prototype to clinical diagnostic testing is demonstrated by generating good quality digital images of malaria-infected blood smears. Further, the acquired slide images have been processed to identify and count the number of malaria-infected red blood cells and thereby perform quantitative parasitemia level estimation. The presented prototype would enable cost-effective deployment of slide-based cyto-diagnostic testing in endemic areas.

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 ...

Fully automated treatment planning for head and neck radiotherapy using a voxel-based dose prediction and dose mimicking method

NASA Astrophysics Data System (ADS)

McIntosh, Chris; Welch, Mattea; McNiven, Andrea; Jaffray, David A.; Purdie, Thomas G.

2017-08-01

Recent works in automated radiotherapy treatment planning have used machine learning based on historical treatment plans to infer the spatial dose distribution for a novel patient directly from the planning image. We present a probabilistic, atlas-based approach which predicts the dose for novel patients using a set of automatically selected most similar patients (atlases). The output is a spatial dose objective, which specifies the desired dose-per-voxel, and therefore replaces the need to specify and tune dose-volume objectives. Voxel-based dose mimicking optimization then converts the predicted dose distribution to a complete treatment plan with dose calculation using a collapsed cone convolution dose engine. In this study, we investigated automated planning for right-sided oropharaynx head and neck patients treated with IMRT and VMAT. We compare four versions of our dose prediction pipeline using a database of 54 training and 12 independent testing patients by evaluating 14 clinical dose evaluation criteria. Our preliminary results are promising and demonstrate that automated methods can generate comparable dose distributions to clinical. Overall, automated plans achieved an average of 0.6% higher dose for target coverage evaluation criteria, and 2.4% lower dose at the organs at risk criteria levels evaluated compared with clinical. There was no statistically significant difference detected in high-dose conformity between automated and clinical plans as measured by the conformation number. Automated plans achieved nine more unique criteria than clinical across the 12 patients tested and automated plans scored a significantly higher dose at the evaluation limit for two high-risk target coverage criteria and a significantly lower dose in one critical organ maximum dose. The novel dose prediction method with dose mimicking can generate complete treatment plans in 12-13 min without user interaction. It is a promising approach for fully automated treatment planning and can be readily applied to different treatment sites and modalities.

Fully automated treatment planning for head and neck radiotherapy using a voxel-based dose prediction and dose mimicking method.

PubMed

McIntosh, Chris; Welch, Mattea; McNiven, Andrea; Jaffray, David A; Purdie, Thomas G

2017-07-06

Recent works in automated radiotherapy treatment planning have used machine learning based on historical treatment plans to infer the spatial dose distribution for a novel patient directly from the planning image. We present a probabilistic, atlas-based approach which predicts the dose for novel patients using a set of automatically selected most similar patients (atlases). The output is a spatial dose objective, which specifies the desired dose-per-voxel, and therefore replaces the need to specify and tune dose-volume objectives. Voxel-based dose mimicking optimization then converts the predicted dose distribution to a complete treatment plan with dose calculation using a collapsed cone convolution dose engine. In this study, we investigated automated planning for right-sided oropharaynx head and neck patients treated with IMRT and VMAT. We compare four versions of our dose prediction pipeline using a database of 54 training and 12 independent testing patients by evaluating 14 clinical dose evaluation criteria. Our preliminary results are promising and demonstrate that automated methods can generate comparable dose distributions to clinical. Overall, automated plans achieved an average of 0.6% higher dose for target coverage evaluation criteria, and 2.4% lower dose at the organs at risk criteria levels evaluated compared with clinical. There was no statistically significant difference detected in high-dose conformity between automated and clinical plans as measured by the conformation number. Automated plans achieved nine more unique criteria than clinical across the 12 patients tested and automated plans scored a significantly higher dose at the evaluation limit for two high-risk target coverage criteria and a significantly lower dose in one critical organ maximum dose. The novel dose prediction method with dose mimicking can generate complete treatment plans in 12-13 min without user interaction. It is a promising approach for fully automated treatment planning and can be readily applied to different treatment sites and modalities.

Fuel Economy Label and CAFE Data Inventory

EPA Pesticide Factsheets

The Fuel Economy Label and CAFE Data asset contains measured summary fuel economy estimates and test data for light-duty vehicle manufacturers by model for certification as required under the Energy Policy and Conservation Act of 1975 (EPCA) and The Energy Independent Security Act of 2007 (EISA) to collect vehicle fuel economy estimates for the creation of Economy Labels and for the calculation of Corporate Average Fuel Economy (CAFE). Manufacturers submit data on an annual basis, or as needed to document vehicle model changes.The EPA performs targeted fuel economy confirmatory tests on approximately 15% of vehicles submitted for validation. Confirmatory data on vehicles is associated with its corresponding submission data to verify the accuracy of manufacturer submissions beyond standard business rules. Submitted data comes in XML format or as documents, with the majority of submissions being sent in XML, and includes descriptive information on the vehicle itself, fuel economy information, and the manufacturer's testing approach. This data may contain proprietary information (CBI) such as information on estimated sales or other data elements indicated by the submitter as confidential. CBI data is not publically available; however, within the EPA data can accessed under the restrictions of the Office of Transportation and Air Quality (OTAQ) CBI policy [RCS Link]. Datasets are segmented by vehicle model/manufacturer and/or year with corresponding fuel economy, te

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.

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.

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.

Standardization of whole slide image morphologic assessment with definition of a new application: Digital slide dynamic morphometry.

PubMed

Puppa, Giacomo; Risio, Mauro; Sheahan, Kieran; Vieth, Michael; Zlobec, Inti; Lugli, Alessandro; Pecori, Sara; Wang, Lai Mun; Langner, Cord; Mitomi, Hiroyuki; Nakamura, Takatoshi; Watanabe, Masahiko; Ueno, Hideki; Chasle, Jacques; Senore, Carlo; Conley, Stephen A; Herlin, Paulette; Lauwers, Gregory Y

2011-01-01

In histopathology, the quantitative assessment of various morphologic features is based on methods originally conceived on specific areas observed through the microscope used. Failure to reproduce the same reference field of view using a different microscope will change the score assessed. Visualization of a digital slide on a screen through a dedicated viewer allows selection of the magnification. However, the field of view is rectangular, unlike the circular field of optical microscopy. In addition, the size of the selected area is not evident, and must be calculated. A digital slide morphometric system was conceived to reproduce the various methods published for assessing tumor budding in colorectal cancer. Eighteen international experts in colorectal cancer were invited to participate in a web-based study by assessing tumor budding with five different methods in 100 digital slides. The specific areas to be tested by each method were marked by colored circles. The areas were grouped in a target-like pattern and then saved as an .xml file. When a digital slide was opened, the .xml file was imported in order to perform the measurements. Since the morphometric tool is composed of layers that can be freely moved on top of the digital slide, the technique was named digital slide dynamic morphometry. Twelve investigators completed the task, the majority of them performing the multiple evaluations of each of the cases in less than 12 minutes. Digital slide dynamic morphometry has various potential applications and might be a useful tool for the assessment of histologic parameters originally conceived for optical microscopy that need to be quantified.

Software design for automated assembly of truss structures

NASA Technical Reports Server (NTRS)

Herstrom, Catherine L.; Grantham, Carolyn; Allen, Cheryl L.; Doggett, William R.; Will, Ralph W.

1992-01-01

Concern over the limited intravehicular activity time has increased the interest in performing in-space assembly and construction operations with automated robotic systems. A technique being considered at LaRC is a supervised-autonomy approach, which can be monitored by an Earth-based supervisor that intervenes only when the automated system encounters a problem. A test-bed to support evaluation of the hardware and software requirements for supervised-autonomy assembly methods was developed. This report describes the design of the software system necessary to support the assembly process. The software is hierarchical and supports both automated assembly operations and supervisor error-recovery procedures, including the capability to pause and reverse any operation. The software design serves as a model for the development of software for more sophisticated automated systems and as a test-bed for evaluation of new concepts and hardware components.

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.

Using the eXtensible Markup Language (XML) in a regional electronic patient record for patients with malignant diseases.

PubMed

Wolff, A C; Mludek, V; van der Haak, M; Bork, W; Bülzebruck, H; Drings, P; Schmücker, P; Wannenmacher, M; Haux, R

2001-01-01

Communication between different institutions which are responsible for the treatment of the same patient is of outstanding significance, especially in the field of tumor diseases. Regional electronic patient records could support the co-operation of different institutions by providing ac-cess to all necessary information whether it belongs to the own institution or to a partner. The Department of Medical Informatics, University of Heidelberg is performing a project in co-operation with the Thoraxclinic-Heidelberg and the Department of Clinical Radiology, University of Heidelberg with the goal: to define an architectural concept for interlinking the electronic patient record of the two clinical institutions to build a common virtual electronic patient record and carry out an exemplary implementation, to examine composition, structure and content of medical documents for tumor patients with the aim of defining an XML-based markup language allowing summarizing overviews and suitable granularities, and to integrate clinical practice guidelines and other external knowledge with the electronic patient record using XML-technologies to support the physician in the daily decision process. This paper will show, how a regional electronic patient record could be built on an architectural level and describe elementary steps towards a on content-oriented structuring of medical records.

Test/score/report: Simulation techniques for automating the test process

NASA Technical Reports Server (NTRS)

Hageman, Barbara H.; Sigman, Clayton B.; Koslosky, John T.

1994-01-01

A Test/Score/Report capability is currently being developed for the Transportable Payload Operations Control Center (TPOCC) Advanced Spacecraft Simulator (TASS) system which will automate testing of the Goddard Space Flight Center (GSFC) Payload Operations Control Center (POCC) and Mission Operations Center (MOC) software in three areas: telemetry decommutation, spacecraft command processing, and spacecraft memory load and dump processing. Automated computer control of the acceptance test process is one of the primary goals of a test team. With the proper simulation tools and user interface, the task of acceptance testing, regression testing, and repeatability of specific test procedures of a ground data system can be a simpler task. Ideally, the goal for complete automation would be to plug the operational deliverable into the simulator, press the start button, execute the test procedure, accumulate and analyze the data, score the results, and report the results to the test team along with a go/no recommendation to the test team. In practice, this may not be possible because of inadequate test tools, pressures of schedules, limited resources, etc. Most tests are accomplished using a certain degree of automation and test procedures that are labor intensive. This paper discusses some simulation techniques that can improve the automation of the test process. The TASS system tests the POCC/MOC software and provides a score based on the test results. The TASS system displays statistics on the success of the POCC/MOC system processing in each of the three areas as well as event messages pertaining to the Test/Score/Report processing. The TASS system also provides formatted reports documenting each step performed during the tests and the results of each step. A prototype of the Test/Score/Report capability is available and currently being used to test some POCC/MOC software deliveries. When this capability is fully operational it should greatly reduce the time necessary to test a POCC/MOC software delivery, as well as improve the quality of the test process.

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

PubMed

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

2017-05-18

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

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.

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…

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…

An automated LS(β)- NaI(Tl)(γ) coincidence system as absolute standard for radioactivity measurements.

PubMed

Joseph, Leena; Das, A P; Ravindra, Anuradha; Kulkarni, D B; Kulkarni, M S

2018-07-01

4πβ-γ coincidence method is a powerful and widely used method to determine the absolute activity concentration of radioactive solutions. A new automated liquid scintillator based coincidence system has been designed, developed, tested and established as absolute standard for radioactivity measurements. The automation is achieved using PLC (programmable logic controller) and SCADA (supervisory control and data acquisition). Radioactive solution of 60 Co was standardized to compare the performance of the automated system with proportional counter based absolute standard maintained in the laboratory. The activity concentrations determined using these two systems were in very good agreement; the new automated system can be used for absolute measurement of activity concentration of radioactive solutions. Copyright © 2018. Published by Elsevier Ltd.

Comparison of two automated instruments for Epstein-Barr virus serology in a large adult hospital and implementation of an Epstein-Barr virus nuclear antigen-based testing algorithm.

PubMed

Al Sidairi, Hilal; Binkhamis, Khalifa; Jackson, Colleen; Roberts, Catherine; Heinstein, Charles; MacDonald, Jimmy; Needle, Robert; Hatchette, Todd F; LeBlanc, Jason J

2017-11-01

Serology remains the mainstay for diagnosis of Epstein-Barr virus (EBV) infection. This study compared two automated platforms (BioPlex 2200 and Architect i2000SR) to test three EBV serological markers: viral capsid antigen (VCA) immunoglobulins of class M (IgM), VCA immunoglobulins of class G (IgG) and EBV nuclear antigen-1 (EBNA-1) IgG. Using sera from 65 patients at various stages of EBV disease, BioPlex demonstrated near-perfect agreement for all EBV markers compared to a consensus reference. The agreement for Architect was near-perfect for VCA IgG and EBNA-1 IgG, and substantial for VCA IgM despite five equivocal results. Since the majority of testing in our hospital was from adults with EBNA-1 IgG positive results, post-implementation analysis of an EBNA-based algorithm showed advantages over parallel testing of the three serologic markers. This small verification demonstrated that both automated systems for EBV serology had good performance for all EBV markers, and an EBNA-based testing algorithm is ideal for an adult hospital.

Hardware fault insertion and instrumentation system: Mechanization and validation

NASA Technical Reports Server (NTRS)

Benson, J. W.

1987-01-01

Automated test capability for extensive low-level hardware fault insertion testing is developed. The test capability is used to calibrate fault detection coverage and associated latency times as relevant to projecting overall system reliability. Described are modifications made to the NASA Ames Reconfigurable Flight Control System (RDFCS) Facility to fully automate the total test loop involving the Draper Laboratories' Fault Injector Unit. The automated capability provided included the application of sequences of simulated low-level hardware faults, the precise measurement of fault latency times, the identification of fault symptoms, and bulk storage of test case results. A PDP-11/60 served as a test coordinator, and a PDP-11/04 as an instrumentation device. The fault injector was controlled by applications test software in the PDP-11/60, rather than by manual commands from a terminal keyboard. The time base was especially developed for this application to use a variety of signal sources in the system simulator.

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.

Automated classification of articular cartilage surfaces based on surface texture.

PubMed

Stachowiak, G P; Stachowiak, G W; Podsiadlo, P

2006-11-01

In this study the automated classification system previously developed by the authors was used to classify articular cartilage surfaces with different degrees of wear. This automated system classifies surfaces based on their texture. Plug samples of sheep cartilage (pins) were run on stainless steel discs under various conditions using a pin-on-disc tribometer. Testing conditions were specifically designed to produce different severities of cartilage damage due to wear. Environmental scanning electron microscope (SEM) (ESEM) images of cartilage surfaces, that formed a database for pattern recognition analysis, were acquired. The ESEM images of cartilage were divided into five groups (classes), each class representing different wear conditions or wear severity. Each class was first examined and assessed visually. Next, the automated classification system (pattern recognition) was applied to all classes. The results of the automated surface texture classification were compared to those based on visual assessment of surface morphology. It was shown that the texture-based automated classification system was an efficient and accurate method of distinguishing between various cartilage surfaces generated under different wear conditions. It appears that the texture-based classification method has potential to become a useful tool in medical diagnostics.

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.

Test-retest reliability of automated whole body and compartmental muscle volume measurements on a wide bore 3T MR system.

PubMed

Thomas, Marianna S; Newman, David; Leinhard, Olof Dahlqvist; Kasmai, Bahman; Greenwood, Richard; Malcolm, Paul N; Karlsson, Anette; Rosander, Johannes; Borga, Magnus; Toms, Andoni P

2014-09-01

To measure the test-retest reproducibility of an automated system for quantifying whole body and compartmental muscle volumes using wide bore 3 T MRI. Thirty volunteers stratified by body mass index underwent whole body 3 T MRI, two-point Dixon sequences, on two separate occasions. Water-fat separation was performed, with automated segmentation of whole body, torso, upper and lower leg volumes, and manually segmented lower leg muscle volumes. Mean automated total body muscle volume was 19·32 L (SD9·1) and 19·28 L (SD9·12) for first and second acquisitions (Intraclass correlation coefficient (ICC) = 1·0, 95% level of agreement -0·32-0·2 L). ICC for all automated test-retest muscle volumes were almost perfect (0·99-1·0) with 95% levels of agreement 1.8-6.6% of mean volume. Automated muscle volume measurements correlate closely with manual quantification (right lower leg: manual 1·68 L (2SD0·6) compared to automated 1·64 L (2SD 0·6), left lower leg: manual 1·69 L (2SD 0·64) compared to automated 1·63 L (SD0·61), correlation coefficients for automated and manual segmentation were 0·94-0·96). Fully automated whole body and compartmental muscle volume quantification can be achieved rapidly on a 3 T wide bore system with very low margins of error, excellent test-retest reliability and excellent correlation to manual segmentation in the lower leg. Sarcopaenia is an important reversible complication of a number of diseases. Manual quantification of muscle volume is time-consuming and expensive. Muscles can be imaged using in and out of phase MRI. Automated atlas-based segmentation can identify muscle groups. Automated muscle volume segmentation is reproducible and can replace manual measurements.

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.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

Verification of an Automated, Digital Dispensing Platform for At-Will Broth Microdilution-Based Antimicrobial Susceptibility Testing.

PubMed

Smith, Kenneth P; Kirby, James E

2016-09-01

With rapid emergence of multidrug-resistant bacteria, there is often a need to perform susceptibility testing for less commonly used or newer antimicrobial agents. Such testing can often be performed only by using labor-intensive, manual dilution methods and lies outside the capacity of most clinical labs, necessitating reference laboratory testing and thereby delaying the availability of susceptibility data. To address the compelling clinical need for microbiology laboratories to perform such testing in-house, we explored a novel, automated, at-will broth microdilution-based susceptibility testing platform. Specifically, we used the modified inkjet printer technology in the HP D300 digital dispensing system to dispense, directly from stock solutions into a 384-well plate, the 2-fold serial dilution series required for broth microdilution testing. This technology was combined with automated absorbance readings and data analysis to determine MICs. Performance was verified by testing members of the Enterobacteriaceae for susceptibility to ampicillin, cefazolin, ciprofloxacin, colistin, gentamicin, meropenem, and tetracycline in comparison to the results obtained with a broth microdilution reference standard. In precision studies, essential and categorical agreement levels were 96.8% and 98.3%, respectively. Furthermore, significantly fewer D300-based measurements were outside ±1 dilution from the modal MIC, suggesting enhanced reproducibility. In accuracy studies performed using a panel of 80 curated clinical isolates, rates of essential and categorical agreement and very major, major, and minor errors were 94%, 96.6%, 0%, 0%, and 3.4%, respectively. Based on these promising initial results, it is anticipated that the D300-based methodology will enable hospital-based clinical microbiology laboratories to perform at-will broth microdilution testing of antimicrobials and to address a critical testing gap. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Optimal Test Design with Rule-Based Item Generation

ERIC Educational Resources Information Center

Geerlings, Hanneke; van der Linden, Wim J.; Glas, Cees A. W.

2013-01-01

Optimal test-design methods are applied to rule-based item generation. Three different cases of automated test design are presented: (a) test assembly from a pool of pregenerated, calibrated items; (b) test generation on the fly from a pool of calibrated item families; and (c) test generation on the fly directly from calibrated features defining…

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

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.

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

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

DDML Schema Validation

DTIC Science & Technology

2016-02-08

Data Display Markup Language HUD heads-up display IRIG Inter-Range Instrumentation Group RCC Range Commanders Council SVG Scalable Vector Graphics...T&E test and evaluation TMATS Telemetry Attributes Transfer Standard XML eXtensible Markup Language DDML Schema Validation, RCC 126-16, February...2016 viii This page intentionally left blank. DDML Schema Validation, RCC 126-16, February 2016 1 1. Introduction This Data Display Markup

76 FR 39090 - Contract Reporting Requirements of Intrastate Natural Gas Companies; Notice of Extension of Time...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-05

... delay until 90 days after the revised Form No. 549D, XML schema format, and Data Dictionary and... Form 549D, the Data Dictionary and Instructions, notice is hereby given that all section 311 and... Data Dictionary and Instructions for filing Form 549D. Staff also corrected and completed testing of a...

An economic evaluation of colorectal cancer screening in primary care practice.

PubMed

Meenan, Richard T; Anderson, Melissa L; Chubak, Jessica; Vernon, Sally W; Fuller, Sharon; Wang, Ching-Yun; Green, Beverly B

2015-06-01

Recent colorectal cancer screening studies focus on optimizing adherence. This study evaluated the cost effectiveness of interventions using electronic health records (EHRs); automated mailings; and stepped support increases to improve 2-year colorectal cancer screening adherence. Analyses were based on a parallel-design, randomized trial in which three stepped interventions (EHR-linked mailings ["automated"]; automated plus telephone assistance ["assisted"]; or automated and assisted plus nurse navigation to testing completion or refusal [navigated"]) were compared to usual care. Data were from August 2008 to November 2011, with analyses performed during 2012-2013. Implementation resources were micro-costed; research and registry development costs were excluded. Incremental cost-effectiveness ratios (ICERs) were based on number of participants current for screening per guidelines over 2 years. Bootstrapping examined robustness of results. Intervention delivery cost per participant current for screening ranged from $21 (automated) to $27 (navigated). Inclusion of induced testing costs (e.g., screening colonoscopy) lowered expenditures for automated (ICER=-$159) and assisted (ICER=-$36) relative to usual care over 2 years. Savings arose from increased fecal occult blood testing, substituting for more expensive colonoscopies in usual care. Results were broadly consistent across demographic subgroups. More intensive interventions were consistently likely to be cost effective relative to less intensive interventions, with willingness to pay values of $600-$1,200 for an additional person current for screening yielding ≥80% probability of cost effectiveness. Two-year cost effectiveness of a stepped approach to colorectal cancer screening promotion based on EHR data is indicated, but longer-term cost effectiveness requires further study. Copyright © 2015 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Toward a New Gold Standard for Early Safety: Automated Temperature-Controlled hERG Test on the PatchLiner®

PubMed Central

Polonchuk, Liudmila

2012-01-01

The Patchliner® temperature-controlled automated patch clamp system was evaluated for testing drug effects on potassium currents through human ether-à-go-go related gene (hERG) channels expressed in Chinese hamster ovary cells at 35–37°C. IC50 values for a set of reference drugs were compared with those obtained using the conventional voltage clamp technique. The results showed good correlation between the data obtained using automated and conventional electrophysiology. Based on these results, the Patchliner® represents an innovative automated electrophysiology platform for conducting the hERG assay that substantially increases throughput and has the advantage of operating at physiological temperature. It allows fast, accurate, and direct assessment of channel function to identify potential proarrhythmic side effects and sets a new standard in ion channel research for drug safety testing. PMID:22303293

Pilot interaction with automated airborne decision making systems

NASA Technical Reports Server (NTRS)

Rouse, W. B.; Hammer, J. M.; Mitchell, C. M.; Morris, N. M.; Lewis, C. M.; Yoon, W. C.

1985-01-01

Progress was made in the three following areas. In the rule-based modeling area, two papers related to identification and significane testing of rule-based models were presented. In the area of operator aiding, research focused on aiding operators in novel failure situations; a discrete control modeling approach to aiding PLANT operators was developed; and a set of guidelines were developed for implementing automation. In the area of flight simulator hardware and software, the hardware will be completed within two months and initial simulation software will then be integrated and tested.

XML-Based SHINE Knowledge Base Interchange Language

NASA Technical Reports Server (NTRS)

James, Mark; Mackey, Ryan; Tikidjian, Raffi

2008-01-01

The SHINE Knowledge Base Interchange Language software has been designed to more efficiently send new knowledge bases to spacecraft that have been embedded with the Spacecraft Health Inference Engine (SHINE) tool. The intention of the behavioral model is to capture most of the information generally associated with a spacecraft functional model, while specifically addressing the needs of execution within SHINE and Livingstone. As such, it has some constructs that are based on one or the other.

Web based aphasia test using service oriented architecture (SOA)

NASA Astrophysics Data System (ADS)

Voos, J. A.; Vigliecca, N. S.; Gonzalez, E. A.

2007-11-01

Based on an aphasia test for Spanish speakers which analyze the patient's basic resources of verbal communication, a web-enabled software was developed to automate its execution. A clinical database was designed as a complement, in order to evaluate the antecedents (risk factors, pharmacological and medical backgrounds, neurological or psychiatric symptoms, brain injury -anatomical and physiological characteristics, etc) which are necessary to carry out a multi-factor statistical analysis in different samples of patients. The automated test was developed following service oriented architecture and implemented in a web site which contains a tests suite, which would allow both integrating the aphasia test with other neuropsychological instruments and increasing the available site information for scientific research. The test design, the database and the study of its psychometric properties (validity, reliability and objectivity) were made in conjunction with neuropsychological researchers, who participate actively in the software design, based on the patients or other subjects of investigation feedback.

Development and verification testing of automation and robotics for assembly of space structures

NASA Technical Reports Server (NTRS)

Rhodes, Marvin D.; Will, Ralph W.; Quach, Cuong C.

1993-01-01

A program was initiated within the past several years to develop operational procedures for automated assembly of truss structures suitable for large-aperture antennas. The assembly operations require the use of a robotic manipulator and are based on the principle of supervised autonomy to minimize crew resources. A hardware testbed was established to support development and evaluation testing. A brute-force automation approach was used to develop the baseline assembly hardware and software techniques. As the system matured and an operation was proven, upgrades were incorprated and assessed against the baseline test results. This paper summarizes the developmental phases of the program, the results of several assembly tests, the current status, and a series of proposed developments for additional hardware and software control capability. No problems that would preclude automated in-space assembly of truss structures have been encountered. The current system was developed at a breadboard level and continued development at an enhanced level is warranted.

Experiments with Test Case Generation and Runtime Analysis

NASA Technical Reports Server (NTRS)

Artho, Cyrille; Drusinsky, Doron; Goldberg, Allen; Havelund, Klaus; Lowry, Mike; Pasareanu, Corina; Rosu, Grigore; Visser, Willem; Koga, Dennis (Technical Monitor)

2003-01-01

Software testing is typically an ad hoc process where human testers manually write many test inputs and expected test results, perhaps automating their execution in a regression suite. This process is cumbersome and costly. This paper reports preliminary results on an approach to further automate this process. The approach consists of combining automated test case generation based on systematically exploring the program's input domain, with runtime analysis, where execution traces are monitored and verified against temporal logic specifications, or analyzed using advanced algorithms for detecting concurrency errors such as data races and deadlocks. The approach suggests to generate specifications dynamically per input instance rather than statically once-and-for-all. The paper describes experiments with variants of this approach in the context of two examples, a planetary rover controller and a space craft fault protection system.

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Red Blood Cell Count Automation Using Microscopic Hyperspectral Imaging Technology.

PubMed

Li, Qingli; Zhou, Mei; Liu, Hongying; Wang, Yiting; Guo, Fangmin

2015-12-01

Red blood cell counts have been proven to be one of the most frequently performed blood tests and are valuable for early diagnosis of some diseases. This paper describes an automated red blood cell counting method based on microscopic hyperspectral imaging technology. Unlike the light microscopy-based red blood count methods, a combined spatial and spectral algorithm is proposed to identify red blood cells by integrating active contour models and automated two-dimensional k-means with spectral angle mapper algorithm. Experimental results show that the proposed algorithm has better performance than spatial based algorithm because the new algorithm can jointly use the spatial and spectral information of blood cells.

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

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.

QuakeML: XML for Seismological Data Exchange and Resource Metadata Description

NASA Astrophysics Data System (ADS)

Euchner, F.; Schorlemmer, D.; Becker, J.; Heinloo, A.; Kästli, P.; Saul, J.; Weber, B.; QuakeML Working Group

2007-12-01

QuakeML is an XML-based data exchange format for seismology that is under development. Current collaborators are from ETH, GFZ, USC, USGS, IRIS DMC, EMSC, ORFEUS, and ISTI. QuakeML development was motivated by the lack of a widely accepted and well-documented data format that is applicable to a broad range of fields in seismology. The development team brings together expertise from communities dealing with analysis and creation of earthquake catalogs, distribution of seismic bulletins, and real-time processing of seismic data. Efforts to merge QuakeML with existing XML dialects are under way. The first release of QuakeML will cover a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Further extensions are in progress or planned, e.g., for macroseismic information, location probability density functions, slip distributions, and ground motion information. The QuakeML language definition is supplemented by a concept to provide resource metadata and facilitate metadata exchange between distributed data providers. For that purpose, we introduce unique, location-independent identifiers of seismological resources. As an application of QuakeML, ETH Zurich currently develops a Python-based seismicity analysis toolkit as a contribution to CSEP (Collaboratory for the Study of Earthquake Predictability). We follow a collaborative and transparent development approach along the lines of the procedures of the World Wide Web Consortium (W3C). QuakeML currently is in working draft status. The standard description will be subjected to a public Request for Comments (RFC) process and eventually reach the status of a recommendation. QuakeML can be found at http://www.quakeml.org.

Definition of an ISO 19115 metadata profile for SeaDataNet II Cruise Summary Reports and its XML encoding

NASA Astrophysics Data System (ADS)

Boldrini, Enrico; Schaap, Dick M. A.; Nativi, Stefano

2013-04-01

SeaDataNet implements a distributed pan-European infrastructure for Ocean and Marine Data Management whose nodes are maintained by 40 national oceanographic and marine data centers from 35 countries riparian to all European seas. A unique portal makes possible distributed discovery, visualization and access of the available sea data across all the member nodes. Geographic metadata play an important role in such an infrastructure, enabling an efficient documentation and discovery of the resources of interest. In particular: - Common Data Index (CDI) metadata describe the sea datasets, including identification information (e.g. product title, interested area), evaluation information (e.g. data resolution, constraints) and distribution information (e.g. download endpoint, download protocol); - Cruise Summary Reports (CSR) metadata describe cruises and field experiments at sea, including identification information (e.g. cruise title, name of the ship), acquisition information (e.g. utilized instruments, number of samples taken) In the context of the second phase of SeaDataNet (SeaDataNet 2 EU FP7 project, grant agreement 283607, started on October 1st, 2011 for a duration of 4 years) a major target is the setting, adoption and promotion of common international standards, to the benefit of outreach and interoperability with the international initiatives and communities (e.g. OGC, INSPIRE, GEOSS, …). A standardization effort conducted by CNR with the support of MARIS, IFREMER, STFC, BODC and ENEA has led to the creation of a ISO 19115 metadata profile of CDI and its XML encoding based on ISO 19139. The CDI profile is now in its stable version and it's being implemented and adopted by the SeaDataNet community tools and software. The effort has then continued to produce an ISO based metadata model and its XML encoding also for CSR. The metadata elements included in the CSR profile belong to different models: - ISO 19115: E.g. cruise identification information, including title and area of interest; metadata responsible party information - ISO 19115-2: E.g. acquisition information, including date of sampling, instruments used - SeaDataNet: E.g. SeaDataNet community specific, including EDMO and EDMERP code lists Two main guidelines have been followed in the metadata model drafting: - All the obligations and constraints required by both the ISO standards and INSPIRE directive had to be satisfied. These include the presence of specific elements with given cardinality (e.g. mandatory metadata date stamp, mandatory lineage information) - All the content information of legacy CSR format had to be supported by the new metadata model. An XML encoding of the CSR profile has been defined as well. Based on the ISO 19139 XML schema and constraints, it adds the new elements specific of the SeaDataNet community. The associated Schematron rules are used to enforce constraints not enforceable just with the Schema and to validate elements content against the SeaDataNet code lists vocabularies.

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

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…

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

FMEA of manual and automated methods for commissioning a radiotherapy treatment planning system.

PubMed

Wexler, Amy; Gu, Bruce; Goddu, Sreekrishna; Mutic, Maya; Yaddanapudi, Sridhar; Olsen, Lindsey; Harry, Taylor; Noel, Camille; Pawlicki, Todd; Mutic, Sasa; Cai, Bin

2017-09-01

To evaluate the level of risk involved in treatment planning system (TPS) commissioning using a manual test procedure, and to compare the associated process-based risk to that of an automated commissioning process (ACP) by performing an in-depth failure modes and effects analysis (FMEA). The authors collaborated to determine the potential failure modes of the TPS commissioning process using (a) approaches involving manual data measurement, modeling, and validation tests and (b) an automated process utilizing application programming interface (API) scripting, preloaded, and premodeled standard radiation beam data, digital heterogeneous phantom, and an automated commissioning test suite (ACTS). The severity (S), occurrence (O), and detectability (D) were scored for each failure mode and the risk priority numbers (RPN) were derived based on TG-100 scale. Failure modes were then analyzed and ranked based on RPN. The total number of failure modes, RPN scores and the top 10 failure modes with highest risk were described and cross-compared between the two approaches. RPN reduction analysis is also presented and used as another quantifiable metric to evaluate the proposed approach. The FMEA of a MTP resulted in 47 failure modes with an RPN ave of 161 and S ave of 6.7. The highest risk process of "Measurement Equipment Selection" resulted in an RPN max of 640. The FMEA of an ACP resulted in 36 failure modes with an RPN ave of 73 and S ave of 6.7. The highest risk process of "EPID Calibration" resulted in an RPN max of 576. An FMEA of treatment planning commissioning tests using automation and standardization via API scripting, preloaded, and pre-modeled standard beam data, and digital phantoms suggests that errors and risks may be reduced through the use of an ACP. © 2017 American Association of Physicists in Medicine.

An Automated, Experimenter-Free Method for the Standardised, Operant Cognitive Testing of Rats

PubMed Central

Rivalan, Marion; Munawar, Humaira; Fuchs, Anna; Winter, York

2017-01-01

Animal models of human pathology are essential for biomedical research. However, a recurring issue in the use of animal models is the poor reproducibility of behavioural and physiological findings within and between laboratories. The most critical factor influencing this issue remains the experimenter themselves. One solution is the use of procedures devoid of human intervention. We present a novel approach to experimenter-free testing cognitive abilities in rats, by combining undisturbed group housing with automated, standardized and individual operant testing. This experimenter-free system consisted of an automated-operant system (Bussey-Saksida rat touch screen) connected to a home cage containing group living rats via an automated animal sorter (PhenoSys). The automated animal sorter, which is based on radio-frequency identification (RFID) technology, functioned as a mechanical replacement of the experimenter. Rats learnt to regularly and individually enter the operant chamber and remained there for the duration of the experimental session only. Self-motivated rats acquired the complex touch screen task of trial-unique non-matching to location (TUNL) in half the time reported for animals that were manually placed into the operant chamber. Rat performance was similar between the two groups within our laboratory, and comparable to previously published results obtained elsewhere. This reproducibility, both within and between laboratories, confirms the validity of this approach. In addition, automation reduced daily experimental time by 80%, eliminated animal handling, and reduced equipment cost. This automated, experimenter-free setup is a promising tool of great potential for testing a large variety of functions with full automation in future studies. PMID:28060883

CIRSS vertical data integration, San Bernardino County study phases 1-A, 1-B

NASA Technical Reports Server (NTRS)

Christenson, J.; Michel, R. (Principal Investigator)

1981-01-01

User needs, data types, data automation, and preliminary applications are described for an effort to assemble a single data base for San Bernardino County from data bases which exist at several administrative levels. Each of the data bases used was registered and converted to a grid-based data file at a resolution of 4 acres and used to create a multivariable data base for the entire study area. To this data base were added classified LANDSAT data from 1976 and 1979. The resulting data base thus integrated in a uniform format all of the separately automated data within the study area. Several possible interactions between existing geocoded data bases and LANDSAT data were tested. The use of LANDSAT to update existing data base is to be tested.

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)

Structure of the Brazilian Sign Language (Libras) for Computational Tools: Citizenship and Social Inclusion

NASA Astrophysics Data System (ADS)

Guimaraes, Cayley; Antunes, Diego R.; de F. Guilhermino Trindade, Daniela; da Silva, Rafaella A. Lopes; Garcia, Laura Sanchez

This work presents a computational model (XML) of the Brazilian Sign Language (Libras), based on its phonology. The model was used to create a sample of representative signs to aid the recording of a base of videos whose aim is to support the development of tools to support genuine social inclusion of the deaf.

77 FR 48527 - National Customs Automation Program (NCAP) Test Concerning Automated Commercial Environment (ACE...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-14

... Program (NCAP) Test Concerning Automated Commercial Environment (ACE) Simplified Entry: Modification of... Automated Commercial Environment (ACE). The test's participant selection criteria are modified to reflect... (NCAP) test concerning Automated Commercial Environment (ACE) Simplified Entry functionality (Simplified...

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

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…

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.…

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.…

Automated Portable Test (APT) System: overview and prospects

NASA Technical Reports Server (NTRS)

Bittner, A. C.; Smith, M. G.; Kennedy, R. S.; Staley, C. F.; Harbeson, M. M.

1985-01-01

The Automated Portable Test (APT) System is a notebook-sized, computer-based, human-performance and subjective-status assessment system. It is now being used in a wide range of environmental studies (e.g., simulator aftereffects, flight tests, drug effects, and hypoxia). Three questionnaires and 15 performance tests have been implemented, and the adaptation of 30 more tests is underway or is planned. The APT System is easily transportable, is inexpensive, and has the breadth of expansion options required for field and laboratory applications. The APT System is a powerful and expandable tool for human assessment in remote and unusual environments.