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

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.

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.

DocML: A Digital Library of University Data.

ERIC Educational Resources Information Center

Papadakis, Ioannis; Karakoidas, Vassileios; Chrissikopoulos, Vassileios

2002-01-01

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

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

DTIC Science & Technology

2009-09-21

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

A 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

Information Model Translation to Support a Wider Science Community

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

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.

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.

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.

A full XML-based approach to creating hypermedia learning modules in web-based environments: application to a pathology course.

PubMed

Staccini, Pascal; Dufour, Jean -Charles; Joubert, Michel; Michiels, Jean -François; Fieschi, Marius

2003-01-01

Nowadays, web-based learning services are a key topic in the pedagogical and learning strategies of universities. While organisational and teaching requirements of the learning environment are being evaluated, technical specifications are emerging, enabling educators to build advanced "units of learning". Changes, however, take a long time and cost-effective solutions have to be found to involve our institutions in such actions. In this paper, we present a model of the components of a course. We detail the method followed to implement this model in hypermedia modules with a viewer that can be played on line or from a CD-ROM. The XML technology has been used to implement all the data structures and a client-side architecture has been designed to build a course viewer. Standards of description of content (such as Dublin Core and DocBook) have been integrated into the data structures. This tool has been populated with data from a pathology course and supports other medical contents. The choice of the architecture and the usefulness of the programming tools are discussed. The means of migrating towards a server-side application are presented.

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 .

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.

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

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.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-03-01

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

A generic, web-based clinical information system architecture using HL7 CDA: successful implementation in dermatological routine care.

PubMed

Schuler, Thilo; Boeker, Martin; Klar, Rüdiger; Müller, Marcel

2007-01-01

The requirements of highly specialized clinical domains are often underrepresented in hospital information systems (HIS). Common consequences are that documentation remains to be paper-based or external systems with insufficient HIS integration are used. This paper presents a solution to overcome this deficiency in the form of a generic framework based on the HL7 Clinical Document Architecture. The central architectural idea is the definition of customized forms using a schema-controlled XML language. These flexible form definitions drive the user interface, the data storage, and standardized data exchange. A successful proof-of-concept application in a dermatologic outpatient wound care department has been implemented, and is well accepted by the clinicians. Our work with HL7 CDA revealed the need for further practical research in the health information standards realm.

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

DTIC Science & Technology

2013-05-01

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

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

PubMed

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

2017-08-01

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

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

PubMed Central

Montón, Luis Gardeazabal

2017-01-01

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

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

PubMed

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

2010-11-15

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

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

PubMed Central

2010-01-01

Background The pathology report of radical prostatectomy specimens plays an important role in clinical decisions and the prognostic evaluation in Prostate Cancer (PCa). The anatomical schema is a helpful tool to document PCa extension for clinical and research purposes. To achieve electronic documentation and analysis, an appropriate documentation model for anatomical schemas is needed. For this purpose we developed cMDX. Methods The document architecture of cMDX was designed according to Open Packaging Conventions by separating the whole data into template data and patient data. Analogue custom XML elements were considered to harmonize the graphical representation (e.g. tumour extension) with the textual data (e.g. histological patterns). The graphical documentation was based on the four-layer visualization model that forms the interaction between different custom XML elements. Sensible personal data were encrypted with a 256-bit cryptographic algorithm to avoid misuse. In order to assess the clinical value, we retrospectively analysed the tumour extension in 255 patients after radical prostatectomy. Results The pathology report with cMDX can represent pathological findings of the prostate in schematic styles. Such reports can be integrated into the hospital information system. "cMDX" documents can be converted into different data formats like text, graphics and PDF. Supplementary tools like cMDX Editor and an analyser tool were implemented. The graphical analysis of 255 prostatectomy specimens showed that PCa were mostly localized in the peripheral zone (Mean: 73% ± 25). 54% of PCa showed a multifocal growth pattern. Conclusions cMDX can be used for routine histopathological reporting of radical prostatectomy specimens and provide data for scientific analysis. PMID:21078179

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.

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

DTIC Science & Technology

2012-09-01

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

A Multi-mission Event-Driven Component-Based System for Support of Flight Software Development, ATLO, and Operations first used by the Mars Science Laboratory (MSL) Project

NASA Technical Reports Server (NTRS)

Dehghani, Navid; Tankenson, Michael

2006-01-01

This viewgraph presentation reviews the architectural description of the Mission Data Processing and Control System (MPCS). MPCS is an event-driven, multi-mission ground data processing components providing uplink, downlink, and data management capabilities which will support the Mars Science Laboratory (MSL) project as its first target mission. MPCS is designed with these factors (1) Enabling plug and play architecture (2) MPCS has strong inheritance from GDS components that have been developed for other Flight Projects (MER, MRO, DAWN, MSAP), and are currently being used in operations and ATLO, and (3) MPCS components are Java-based, platform independent, and are designed to consume and produce XML-formatted data

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.

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.

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

DTIC Science & Technology

2013-09-01

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

Design and implementation of workflow engine for service-oriented architecture

NASA Astrophysics Data System (ADS)

Peng, Shuqing; Duan, Huining; Chen, Deyun

2009-04-01

As computer network is developed rapidly and in the situation of the appearance of distribution specialty in enterprise application, traditional workflow engine have some deficiencies, such as complex structure, bad stability, poor portability, little reusability and difficult maintenance. In this paper, in order to improve the stability, scalability and flexibility of workflow management system, a four-layer architecture structure of workflow engine based on SOA is put forward according to the XPDL standard of Workflow Management Coalition, the route control mechanism in control model is accomplished and the scheduling strategy of cyclic routing and acyclic routing is designed, and the workflow engine which adopts the technology such as XML, JSP, EJB and so on is implemented.

EASEE: an open architecture approach for modeling battlespace signal and sensor phenomenology

NASA Astrophysics Data System (ADS)

Waldrop, Lauren E.; Wilson, D. Keith; Ekegren, Michael T.; Borden, Christian T.

2017-04-01

Open architecture in the context of defense applications encourages collaboration across government agencies and academia. This paper describes a success story in the implementation of an open architecture framework that fosters transparency and modularity in the context of Environmental Awareness for Sensor and Emitter Employment (EASEE), a complex physics-based software package for modeling the effects of terrain and atmospheric conditions on signal propagation and sensor performance. Among the highlighted features in this paper are: (1) a code refactorization to separate sensitive parts of EASEE, thus allowing collaborators the opportunity to view and interact with non-sensitive parts of the EASEE framework with the end goal of supporting collaborative innovation, (2) a data exchange and validation effort to enable the dynamic addition of signatures within EASEE thus supporting a modular notion that components can be easily added or removed to the software without requiring recompilation by developers, and (3) a flexible and extensible XML interface, which aids in decoupling graphical user interfaces from EASEE's calculation engine, and thus encourages adaptability to many different defense applications. In addition to the outlined points above, this paper also addresses EASEE's ability to interface with both proprietary systems such as ArcGIS. A specific use case regarding the implementation of an ArcGIS toolbar that leverages EASEE's XML interface and enables users to set up an EASEE-compliant configuration for probability of detection or optimal sensor placement calculations in various modalities is discussed as well.

Reference Architecture for MNE 5 Technical System

DTIC Science & Technology

2007-05-30

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

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

Enterprise-wide PACS: beyond radiology, an architecture to manage all medical images.

PubMed

Bandon, David; Lovis, Christian; Geissbühler, Antoine; Vallée, Jean-Paul

2005-08-01

Picture archiving and communication systems (PACS) have the vocation to manage all medical images acquired within the hospital. To address the various situations encountered in the imaging specialties, the traditional architecture used for the radiology department has to evolve. We present our preliminarily results toward an enterprise-wide PACS intended to support all kind of image production in medicine, from biomolecular images to whole-body pictures. Our solution is based on an existing radiologic PACS system from which images are distributed through an electronic patient record to all care facilities. This platform is enriched with a flexible integration framework supporting digital image communication in medicine (DICOM) and DICOM-XML formats. In addition, a generic workflow engine highly customizable is used to drive work processes. Echocardiology; hematology; ear, nose, and throat; and dermatology, including wounds, follow-up is the first implemented extensions outside of radiology. We also propose a global strategy for further developments based on three possible architectures for an enterprise-wide PACS.

Architecture of a spatial data service system for statistical analysis and visualization of regional climate changes

NASA Astrophysics Data System (ADS)

Titov, A. G.; Okladnikov, I. G.; Gordov, E. P.

2017-11-01

The use of large geospatial datasets in climate change studies requires the development of a set of Spatial Data Infrastructure (SDI) elements, including geoprocessing and cartographical visualization web services. This paper presents the architecture of a geospatial OGC web service system as an integral part of a virtual research environment (VRE) general architecture for statistical processing and visualization of meteorological and climatic data. The architecture is a set of interconnected standalone SDI nodes with corresponding data storage systems. Each node runs a specialized software, such as a geoportal, cartographical web services (WMS/WFS), a metadata catalog, and a MySQL database of technical metadata describing geospatial datasets available for the node. It also contains geospatial data processing services (WPS) based on a modular computing backend realizing statistical processing functionality and, thus, providing analysis of large datasets with the results of visualization and export into files of standard formats (XML, binary, etc.). Some cartographical web services have been developed in a system’s prototype to provide capabilities to work with raster and vector geospatial data based on OGC web services. The distributed architecture presented allows easy addition of new nodes, computing and data storage systems, and provides a solid computational infrastructure for regional climate change studies based on modern Web and GIS technologies.

End-to-end network models encompassing terrestrial, wireless, and satellite components

NASA Astrophysics Data System (ADS)

Boyarko, Chandler L.; Britton, John S.; Flores, Phil E.; Lambert, Charles B.; Pendzick, John M.; Ryan, Christopher M.; Shankman, Gordon L.; Williams, Ramon P.

2004-08-01

Development of network models that reflect true end-to-end architectures such as the Transformational Communications Architecture need to encompass terrestrial, wireless and satellite component to truly represent all of the complexities in a world wide communications network. Use of best-in-class tools including OPNET, Satellite Tool Kit (STK), Popkin System Architect and their well known XML-friendly definitions, such as OPNET Modeler's Data Type Description (DTD), or socket-based data transfer modules, such as STK/Connect, enable the sharing of data between applications for more rapid development of end-to-end system architectures and a more complete system design. By sharing the results of and integrating best-in-class tools we are able to (1) promote sharing of data, (2) enhance the fidelity of our results and (3) allow network and application performance to be viewed in the context of the entire enterprise and its processes.

A Role for Semantic Web Technologies in Patient Record Data Collection

NASA Astrophysics Data System (ADS)

Ogbuji, Chimezie

Business Process Management Systems (BPMS) are a component of the stack of Web standards that comprise Service Oriented Architecture (SOA). Such systems are representative of the architectural framework of modern information systems built in an enterprise intranet and are in contrast to systems built for deployment on the larger World Wide Web. The REST architectural style is an emerging style for building loosely coupled systems based purely on the native HTTP protocol. It is a coordinated set of architectural constraints with a goal to minimize latency, maximize the independence and scalability of distributed components, and facilitate the use of intermediary processors.Within the development community for distributed, Web-based systems, there has been a debate regarding themerits of both approaches. In some cases, there are legitimate concerns about the differences in both architectural styles. In other cases, the contention seems to be based on concerns that are marginal at best. In this chapter, we will attempt to contribute to this debate by focusing on a specific, deployed use case that emphasizes the role of the Semantic Web, a simple Web application architecture that leverages the use of declarative XML processing, and the needs of a workflow system. The use case involves orchestrating a work process associated with the data entry of structured patient record content into a research registry at the Cleveland Clinic's Clinical Investigation department in the Heart and Vascular Institute.

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.

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

NASA Astrophysics Data System (ADS)

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

2002-05-01

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

An intersubject variable regional anesthesia simulator with a virtual patient architecture.

PubMed

Ullrich, Sebastian; Grottke, Oliver; Fried, Eduard; Frommen, Thorsten; Liao, Wei; Rossaint, Rolf; Kuhlen, Torsten; Deserno, Thomas M

2009-11-01

The main purpose is to provide an intuitive VR-based training environment for regional anesthesia (RA). The research question is how to process subject-specific datasets, organize them in a meaningful way and how to perform the simulation for peripheral regions. We propose a flexible virtual patient architecture and methods to process datasets. Image acquisition, image processing (especially segmentation), interactive nerve modeling and permutations (nerve instantiation) are described in detail. The simulation of electric impulse stimulation and according responses are essential for the training of peripheral RA and solved by an approach based on the electric distance. We have created an XML-based virtual patient database with several subjects. Prototypes of the simulation are implemented and run on multimodal VR hardware (e.g., stereoscopic display and haptic device). A first user pilot study has confirmed our approach. The virtual patient architecture enables support for arbitrary scenarios on different subjects. This concept can also be used for other simulators. In future work, we plan to extend the simulation and conduct further evaluations in order to provide a tool for routine training for RA.

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.

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

PubMed

Rojas-Barahona, L M; Giorgino, T

2009-04-01

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

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

There is a need in clinical and research settings for a sophisticated, generalized, web based survey tool that supports complex logic, separation of content and presentation, and computable guidelines. There are many commercial and open source survey packages available that provide simple logic; few provide sophistication beyond “goto” statements; none support the use of guidelines. These tools are driven by databases, static web pages, and structured documents using markup languages such as eXtensible Markup Language (XML). We propose a generalized, guideline aware language and an implementation architecture using open source standards.

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.

Clinical Documents: Attribute-Values Entity Representation, Context, Page Layout And Communication

PubMed Central

Lovis, Christian; Lamb, Alexander; Baud, Robert; Rassinoux, Anne-Marie; Fabry, Paul; Geissbühler, Antoine

2003-01-01

This paper presents how acquisition, storage and communication of clinical documents are implemented at the University Hospitals of Geneva. Careful attention has been given to user-interfaces, in order to support complex layouts, spell checking, templates management with automatic prefilling in order to facilitate acquisition. A dual architecture has been developed for storage using an attributes-values entity unified database and a consolidated, patient-centered, layout-respectful files-based storage, providing both representation power and sinsert (peed of accesses. This architecture allows great flexibility to store a continuum of data types from simple type values up to complex clinical reports. Finally, communication is entirely based on HTTP-XML internally and a HL-7 CDA interface V2 is currently studied for external communication. Some of the problem encountered, mostly concerning the typology of documents and the ontology of clinical attributes are evoked. PMID:14728202

The Use of HepRep in GLAST

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

Perl, Joseph

2003-07-10

HepRep is a generic, hierarchical format for description of graphics representables that can be augmented by physics information and relational properties. It was developed for high energy physics event display applications and is especially suited to client/server or component frameworks. The GLAST experiment, an international effort led by NASA for a gamma-ray telescope to launch in 2006, chose HepRep to provide a flexible, extensible and maintainable framework for their event display without tying their users to any one graphics application. To support HepRep in their GUADI infrastructure, GLAST developed a HepRep filler and builder architecture. The architecture hides the detailsmore » of XML and CORBA in a set of base and helper classes allowing physics experts to focus on what data they want to represent. GLAST has two GAUDI services: HepRepSvc, which registers HepRep fillers in a global registry and allows the HepRep to be exported to XML, and CorbaSvc, which allows the HepRep to be published through a CORBA interface and which allows the client application to feed commands back to GAUDI (such as start next event, or run some GAUDI algorithm). GLAST's HepRep solution gives users a choice of client applications, WIRED (written in Java) or FRED (written in C++ and Ruby), and leaves them free to move to any future HepRep-compliant event display.« less

Instrument Remote Control via the Astronomical Instrument Markup Language

NASA Technical Reports Server (NTRS)

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

1998-01-01

The Instrument Remote Control (IRC) project ongoing at NASA's Goddard Space Flight Center's (GSFC) Information Systems Center (ISC) supports NASA's mission by defining an adaptive intranet-based framework that provides robust interactive and distributed control and monitoring of remote instruments. An astronomical IRC architecture that combines the platform-independent processing capabilities of Java with the power of Extensible Markup Language (XML) to express hierarchical data in an equally platform-independent, as well as human readable manner, has been developed. This architecture is implemented using a variety of XML support tools and Application Programming Interfaces (API) written in Java. IRC will enable trusted astronomers from around the world to easily access infrared instruments (e.g., telescopes, cameras, and spectrometers) located in remote, inhospitable environments, such as the South Pole, a high Chilean mountaintop, or an airborne observatory aboard a Boeing 747. Using IRC's frameworks, an astronomer or other scientist can easily define the type of onboard instrument, control the instrument remotely, and return monitoring data all through the intranet. The Astronomical Instrument Markup Language (AIML) is the first implementation of the more general Instrument Markup Language (IML). The key aspects of our approach to instrument description and control applies to many domains, from medical instruments to machine assembly lines. The concepts behind AIML apply equally well to the description and control of instruments in general. IRC enables us to apply our techniques to several instruments, preferably from different observatories.

ALMA software architecture

NASA Astrophysics Data System (ADS)

Schwarz, Joseph; Raffi, Gianni

2002-12-01

The Atacama Large Millimeter Array (ALMA) is a joint project involving astronomical organizations in Europe and North America. ALMA will consist of at least 64 12-meter antennas operating in the millimeter and sub-millimeter range. It will be located at an altitude of about 5000m in the Chilean Atacama desert. The primary challenge to the development of the software architecture is the fact that both its development and runtime environments will be distributed. Groups at different institutes will develop the key elements such as Proposal Preparation tools, Instrument operation, On-line calibration and reduction, and Archiving. The Proposal Preparation software will be used primarily at scientists' home institutions (or on their laptops), while Instrument Operations will execute on a set of networked computers at the ALMA Operations Support Facility. The ALMA Science Archive, itself to be replicated at several sites, will serve astronomers worldwide. Building upon the existing ALMA Common Software (ACS), the system architects will prepare a robust framework that will use XML-encoded entity objects to provide an effective solution to the persistence needs of this system, while remaining largely independent of any underlying DBMS technology. Independence of distributed subsystems will be facilitated by an XML- and CORBA-based pass-by-value mechanism for exchange of objects. Proof of concept (as well as a guide to subsystem developers) will come from a prototype whose details will be presented.

Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

NASA Astrophysics Data System (ADS)

Lahinta, A.; Haris, I.; Abdillah, T.

2017-03-01

The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

Distributed Learning Metadata Standards

ERIC Educational Resources Information Center

McClelland, Marilyn

2004-01-01

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

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.

An Extensible Information Grid for Risk Management

NASA Technical Reports Server (NTRS)

Maluf, David A.; Bell, David G.

2003-01-01

This paper describes recent work on developing an extensible information grid for risk management at NASA - a RISK INFORMATION GRID. This grid is being developed by integrating information grid technology with risk management processes for a variety of risk related applications. To date, RISK GRID applications are being developed for three main NASA processes: risk management - a closed-loop iterative process for explicit risk management, program/project management - a proactive process that includes risk management, and mishap management - a feedback loop for learning from historical risks that escaped other processes. This is enabled through an architecture involving an extensible database, structuring information with XML, schemaless mapping of XML, and secure server-mediated communication using standard protocols.

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

XWeB: The XML Warehouse Benchmark

NASA Astrophysics Data System (ADS)

Mahboubi, Hadj; Darmont, Jérôme

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

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.

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.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

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

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

PubMed

Masseroli, Marco; Marchente, Mario

2008-07-01

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

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

PubMed

Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

2012-03-01

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

XML technology planning database : lessons learned

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Neff, Jon M.

2005-01-01

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

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

PubMed

Saadawi, Gilan M; Harrison, James H

2006-10-01

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

Web-based Traffic Noise Control Support System for Sustainable Transportation

NASA Astrophysics Data System (ADS)

Fan, Lisa; Dai, Liming; Li, Anson

Traffic noise is considered as one of the major pollutions that will affect our communities in the future. This paper presents a framework of web-based traffic noise control support system (WTNCSS) for a sustainable transportation. WTNCSS is to provide the decision makers, engineers and publics a platform to efficiently access the information, and effectively making decisions related to traffic control. The system is based on a Service Oriented Architecture (SOA) which takes the advantages of the convenience of World Wide Web system with the data format of XML. The whole system is divided into different modules such as the prediction module, ontology-based expert module and dynamic online survey module. Each module of the system provides a distinct information service to the decision support center through the HTTP protocol.

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.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

Video sensor architecture for surveillance applications.

PubMed

Sánchez, Jordi; Benet, Ginés; Simó, José E

2012-01-01

This paper introduces a flexible hardware and software architecture for a smart video sensor. This sensor has been applied in a video surveillance application where some of these video sensors are deployed, constituting the sensory nodes of a distributed surveillance system. In this system, a video sensor node processes images locally in order to extract objects of interest, and classify them. The sensor node reports the processing results to other nodes in the cloud (a user or higher level software) in the form of an XML description. The hardware architecture of each sensor node has been developed using two DSP processors and an FPGA that controls, in a flexible way, the interconnection among processors and the image data flow. The developed node software is based on pluggable components and runs on a provided execution run-time. Some basic and application-specific software components have been developed, in particular: acquisition, segmentation, labeling, tracking, classification and feature extraction. Preliminary results demonstrate that the system can achieve up to 7.5 frames per second in the worst case, and the true positive rates in the classification of objects are better than 80%.

Video Sensor Architecture for Surveillance Applications

PubMed Central

Sánchez, Jordi; Benet, Ginés; Simó, José E.

2012-01-01

This paper introduces a flexible hardware and software architecture for a smart video sensor. This sensor has been applied in a video surveillance application where some of these video sensors are deployed, constituting the sensory nodes of a distributed surveillance system. In this system, a video sensor node processes images locally in order to extract objects of interest, and classify them. The sensor node reports the processing results to other nodes in the cloud (a user or higher level software) in the form of an XML description. The hardware architecture of each sensor node has been developed using two DSP processors and an FPGA that controls, in a flexible way, the interconnection among processors and the image data flow. The developed node software is based on pluggable components and runs on a provided execution run-time. Some basic and application-specific software components have been developed, in particular: acquisition, segmentation, labeling, tracking, classification and feature extraction. Preliminary results demonstrate that the system can achieve up to 7.5 frames per second in the worst case, and the true positive rates in the classification of objects are better than 80%. PMID:22438723

Using XML and Java for Astronomical Instrumentation Control

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

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.

iSMART: Ontology-based Semantic Query of CDA Documents

PubMed Central

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

2009-01-01

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

Integration of Geographical Information Systems and Geophysical Applications with Distributed Computing Technologies.

NASA Astrophysics Data System (ADS)

Pierce, M. E.; Aktas, M. S.; Aydin, G.; Fox, G. C.; Gadgil, H.; Sayar, A.

2005-12-01

We examine the application of Web Service Architectures and Grid-based distributed computing technologies to geophysics and geo-informatics. We are particularly interested in the integration of Geographical Information System (GIS) services with distributed data mining applications. GIS services provide the general purpose framework for building archival data services, real time streaming data services, and map-based visualization services that may be integrated with data mining and other applications through the use of distributed messaging systems and Web Service orchestration tools. Building upon on our previous work in these areas, we present our current research efforts. These include fundamental investigations into increasing XML-based Web service performance, supporting real time data streams, and integrating GIS mapping tools with audio/video collaboration systems for shared display and annotation.

VisPort: Web-Based Access to Community-Specific Visualization Functionality [Shedding New Light on Exploding Stars: Visualization for TeraScale Simulation of Neutrino-Driven Supernovae (Final Technical Report)

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

Baker, M Pauline

2007-06-30

The VisPort visualization portal is an experiment in providing Web-based access to visualization functionality from any place and at any time. VisPort adopts a service-oriented architecture to encapsulate visualization functionality and to support remote access. Users employ browser-based client applications to choose data and services, set parameters, and launch visualization jobs. Visualization products typically images or movies are viewed in the user's standard Web browser. VisPort emphasizes visualization solutions customized for specific application communities. Finally, VisPort relies heavily on XML, and introduces the notion of visualization informatics - the formalization and specialization of information related to the process and productsmore » of visualization.« less

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

NASA Astrophysics Data System (ADS)

Singh, Kulwinder; Park, Dong-Won

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

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

Excavator Design Validation

NASA Technical Reports Server (NTRS)

Pholsiri, Chalongrath; English, James; Seberino, Charles; Lim, Yi-Je

2010-01-01

The Excavator Design Validation tool verifies excavator designs by automatically generating control systems and modeling their performance in an accurate simulation of their expected environment. Part of this software design includes interfacing with human operations that can be included in simulation-based studies and validation. This is essential for assessing productivity, versatility, and reliability. This software combines automatic control system generation from CAD (computer-aided design) models, rapid validation of complex mechanism designs, and detailed models of the environment including soil, dust, temperature, remote supervision, and communication latency to create a system of high value. Unique algorithms have been created for controlling and simulating complex robotic mechanisms automatically from just a CAD description. These algorithms are implemented as a commercial cross-platform C++ software toolkit that is configurable using the Extensible Markup Language (XML). The algorithms work with virtually any mobile robotic mechanisms using module descriptions that adhere to the XML standard. In addition, high-fidelity, real-time physics-based simulation algorithms have also been developed that include models of internal forces and the forces produced when a mechanism interacts with the outside world. This capability is combined with an innovative organization for simulation algorithms, new regolith simulation methods, and a unique control and study architecture to make powerful tools with the potential to transform the way NASA verifies and compares excavator designs. Energid's Actin software has been leveraged for this design validation. The architecture includes parametric and Monte Carlo studies tailored for validation of excavator designs and their control by remote human operators. It also includes the ability to interface with third-party software and human-input devices. Two types of simulation models have been adapted: high-fidelity discrete element models and fast analytical models. By using the first to establish parameters for the second, a system has been created that can be executed in real time, or faster than real time, on a desktop PC. This allows Monte Carlo simulations to be performed on a computer platform available to all researchers, and it allows human interaction to be included in a real-time simulation process. Metrics on excavator performance are established that work with the simulation architecture. Both static and dynamic metrics are included.

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.

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

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

Beyond the New Architectures - Enabling Rapid System Configurations

NASA Technical Reports Server (NTRS)

Smith, Dan

2009-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

Naito, O.

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

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…

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.

Integrating hospital information systems in healthcare institutions: a mediation architecture.

PubMed

El Azami, Ikram; Cherkaoui Malki, Mohammed Ouçamah; Tahon, Christian

2012-10-01

Many studies have examined the integration of information systems into healthcare institutions, leading to several standards in the healthcare domain (CORBAmed: Common Object Request Broker Architecture in Medicine; HL7: Health Level Seven International; DICOM: Digital Imaging and Communications in Medicine; and IHE: Integrating the Healthcare Enterprise). Due to the existence of a wide diversity of heterogeneous systems, three essential factors are necessary to fully integrate a system: data, functions and workflow. However, most of the previous studies have dealt with only one or two of these factors and this makes the system integration unsatisfactory. In this paper, we propose a flexible, scalable architecture for Hospital Information Systems (HIS). Our main purpose is to provide a practical solution to insure HIS interoperability so that healthcare institutions can communicate without being obliged to change their local information systems and without altering the tasks of the healthcare professionals. Our architecture is a mediation architecture with 3 levels: 1) a database level, 2) a middleware level and 3) a user interface level. The mediation is based on two central components: the Mediator and the Adapter. Using the XML format allows us to establish a structured, secured exchange of healthcare data. The notion of medical ontology is introduced to solve semantic conflicts and to unify the language used for the exchange. Our mediation architecture provides an effective, promising model that promotes the integration of hospital information systems that are autonomous, heterogeneous, semantically interoperable and platform-independent.

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.

Simulink-Based Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV)

NASA Technical Reports Server (NTRS)

Christhilf, David m.; Bacon, Barton J.

2006-01-01

The Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV) is a Simulink-based approach to providing an engineering quality desktop simulation capability for finding trim solutions, extracting linear models for vehicle analysis and control law development, and generating open-loop and closed-loop time history responses for control system evaluation. It represents a useful level of maturity rather than a finished product. The layout is hierarchical and supports concurrent component development and validation, with support from the Concurrent Versions System (CVS) software management tool. Real Time Workshop (RTW) is used to generate pre-compiled code for substantial component modules, and templates permit switching seamlessly between original Simulink and code compiled for various platforms. Two previous limitations are addressed. Turn around time for incorporating tabular model components was improved through auto-generation of required Simulink diagrams based on data received in XML format. The layout was modified to exploit a Simulink "compile once, evaluate multiple times" capability for zero elapsed time for use in trimming and linearizing. Trim is achieved through a Graphical User Interface (GUI) with a narrow, script definable interface to the vehicle model which facilitates incorporating new models.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

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

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.

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

The ALMA software architecture

NASA Astrophysics Data System (ADS)

Schwarz, Joseph; Farris, Allen; Sommer, Heiko

2004-09-01

The software for the Atacama Large Millimeter Array (ALMA) is being developed by many institutes on two continents. The software itself will function in a distributed environment, from the 0.5-14 kmbaselines that separate antennas to the larger distances that separate the array site at the Llano de Chajnantor in Chile from the operations and user support facilities in Chile, North America and Europe. Distributed development demands 1) interfaces that allow separated groups to work with minimal dependence on their counterparts at other locations; and 2) a common architecture to minimize duplication and ensure that developers can always perform similar tasks in a similar way. The Container/Component model provides a blueprint for the separation of functional from technical concerns: application developers concentrate on implementing functionality in Components, which depend on Containers to provide them with services such as access to remote resources, transparent serialization of entity objects to XML, logging, error handling and security. Early system integrations have verified that this architecture is sound and that developers can successfully exploit its features. The Containers and their services are provided by a system-orienteddevelopment team as part of the ALMA Common Software (ACS), middleware that is based on CORBA.

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

PDB data curation.

PubMed

Wang, Yanchao; Sunderraman, Rajshekhar

2006-01-01

In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation. The other one, PDB Data Curation System with XCML, is designed for further curation which adds four more parts, PDB-XML, PDB, OODB, Protin-OODB, into the previous one. This architecture uses XCML language to automatically check errors of PDB data that enables PDB data more consistent and accurate. These two tools can be used for cleaning existing PDB files and creating new PDB files. We also show some ideas how to add constraints and assertions with XCML to get better data. In addition, we discuss the data provenance that may affect data accuracy and consistency.

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

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…

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 ...

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.

The research and implementation of PDM systems based on the .NET platform

NASA Astrophysics Data System (ADS)

Gao, Hong-li; Jia, Ying-lian; Yang, Ji-long; Jiang, Wei

2005-12-01

A new kind of PDM system scheme based on the .NET platform for solving application problems of the current PDM system applied in an enterprise is described. The key technologies of this system, such as .NET, Accessing Data, information processing, Web, ect., were discussed. The 3-tier architecture of a PDM system based on the C/S and B/S mixed mode was presented. In this system, all users share the same Database Server in order to ensure the coherence and safety of client data. ADO.NET leverages the power of XML to provide disconnected access to data, which frees the connection to be used by other clients. Using this approach, the system performance was improved. Moreover, the important function modules in a PDM system such as project management, product structure management and Document Management module were developed and realized.

Using XML and Java Technologies for Astronomical Instrument Control

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Using XML and Java for Astronomical Instrument Control

NASA Astrophysics Data System (ADS)

Koons, L.; Ames, T.; Evans, R.; Warsaw, C.; Sall, K.

1999-12-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests. Instrument description is too tightly coupled with details of implementation. NASA/Goddard Space Flight Center and AppNet, Inc. are developing a very general and highly extensible framework that applies to virtually any kind of instrument that can be controlled by a computer (e.g., telescopes, microscopes and printers). A key aspect of the object-oriented architecture, implemented in Java, involves software that is driven by an instrument description. The Astronomical Instrument Markup Language (AIML) is a domain-specific implementation of the more generalized Instrument Markup Language (IML). The software architecture combines the platform-independent processing capabilities of Java with the vendor-independent data description syntax of Extensible Markup Language (XML), a human-readable and machine-understandable way to describe structured data. IML is used to describe command sets (including parameters, datatypes, and constraints) and their associated formats, telemetry, and communication mechanisms. The software uses this description to present graphical user interfaces to control and monitor the instrument. Recent efforts have extended to command procedures (scripting) and representation of data pipeline inputs, outputs, and connections. Near future efforts are likely to include an XML description of data visualizations, as well as the potential use of XSL (Extensible Stylesheet Language) to permit astronomers to customize the user interface on several levels: per user, instrument, subsystem, or observatory-wide. Our initial prototyping effort was targeted for HAWC (High-resolution Airborne Wideband Camera), a first-light instrument of SOFIA (the Stratospheric Observatory for Infrared Astronomy). A production-level application of this technology is for one of the three candidate detectors of SPIRE (Spectral and Photometric Imaging REceiver), a focal plane instrument proposed for the European Space Agency's Far Infrared Space Telescope. The detectors are being developed by the Infrared Astrophysics Branch of NASA/GSFC.

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

Federated querying architecture with clinical & translational health IT application.

PubMed

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

2011-10-01

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

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…

Architecture of portable electronic medical records system integrated with streaming media.

PubMed

Chen, Wei; Shih, Chien-Chou

2012-02-01

Due to increasing occurrence of accidents and illness during business trips, travel, or overseas studies, the requirement for portable EMR (Electronic Medical Records) has increased. This study proposes integrating streaming media technology into the EMR system to facilitate referrals, contracted laboratories, and disease notification among hospitals. The current study encoded static and dynamic medical images of patients into a streaming video format and stored them in a Flash Media Server (FMS). Based on the Taiwan Electronic Medical Record Template (TMT) standard, EMR records can be converted into XML documents and used to integrate description fields with embedded streaming videos. This investigation implemented a web-based portable EMR interchanging system using streaming media techniques to expedite exchanging medical image information among hospitals. The proposed architecture of the portable EMR retrieval system not only provides local hospital users the ability to acquire EMR text files from a previous hospital, but also helps access static and dynamic medical images as reference for clinical diagnosis and treatment. The proposed method protects property rights of medical images through information security mechanisms of the Medical Record Interchange Service Center and Health Certificate Authorization to facilitate proper, efficient, and continuous treatment of patients.

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.

In-field Access to Geoscientific Metadata through GPS-enabled Mobile Phones

NASA Astrophysics Data System (ADS)

Hobona, Gobe; Jackson, Mike; Jordan, Colm; Butchart, Ben

2010-05-01

Fieldwork is an integral part of much geosciences research. But whilst geoscientists have physical or online access to data collections whilst in the laboratory or at base stations, equivalent in-field access is not standard or straightforward. The increasing availability of mobile internet and GPS-supported mobile phones, however, now provides the basis for addressing this issue. The SPACER project was commissioned by the Rapid Innovation initiative of the UK Joint Information Systems Committee (JISC) to explore the potential for GPS-enabled mobile phones to access geoscientific metadata collections. Metadata collections within the geosciences and the wider geospatial domain can be disseminated through web services based on the Catalogue Service for Web(CSW) standard of the Open Geospatial Consortium (OGC) - a global grouping of over 380 private, public and academic organisations aiming to improve interoperability between geospatial technologies. CSW offers an XML-over-HTTP interface for querying and retrieval of geospatial metadata. By default, the metadata returned by CSW is based on the ISO19115 standard and encoded in XML conformant to ISO19139. The SPACER project has created a prototype application that enables mobile phones to send queries to CSW containing user-defined keywords and coordinates acquired from GPS devices built-into the phones. The prototype has been developed using the free and open source Google Android platform. The mobile application offers views for listing titles, presenting multiple metadata elements and a Google Map with an overlay of bounding coordinates of datasets. The presentation will describe the architecture and approach applied in the development of the prototype.

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.

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.

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.

Naval Open Architecture Contract Guidebook for Program Managers

DTIC Science & Technology

2010-06-30

a whole, transform inputs into outputs. [IEEE/EIA Std. 12207 /1997] “APP233/ ISO 10303” – APP233 an “Application Protocol” for Systems Engineering...Language Metadata Interchange (XMI) and AP233/ ISO 10303). The contractor shall identify the proposed standards and formats to be used. The contractor...ANSI ISO /IEC 9075-1, ISO /IEC 9075-2, ISO /IEC 9075-3, ISO /IEC 9075-4, ISO /IEC 9075-5) 2. HTML for presentation layer (e.g., XML 1.0

CCSDS Overview

NASA Technical Reports Server (NTRS)

Kearney, Mike

2013-01-01

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

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

DTIC Science & Technology

2005-02-01

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

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.

A new service-oriented grid-based method for AIoT application and implementation

NASA Astrophysics Data System (ADS)

Zou, Yiqin; Quan, Li

2017-07-01

The traditional three-layer Internet of things (IoT) model, which includes physical perception layer, information transferring layer and service application layer, cannot express complexity and diversity in agricultural engineering area completely. It is hard to categorize, organize and manage the agricultural things with these three layers. Based on the above requirements, we propose a new service-oriented grid-based method to set up and build the agricultural IoT. Considering the heterogeneous, limitation, transparency and leveling attributes of agricultural things, we propose an abstract model for all agricultural resources. This model is service-oriented and expressed with Open Grid Services Architecture (OGSA). Information and data of agricultural things were described and encapsulated by using XML in this model. Every agricultural engineering application will provide service by enabling one application node in this service-oriented grid. Description of Web Service Resource Framework (WSRF)-based Agricultural Internet of Things (AIoT) and the encapsulation method were also discussed in this paper for resource management in this model.

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.

Experiences with the Application of Services Oriented Approaches to the Federation of Heterogeneous Geologic Data Resources

NASA Astrophysics Data System (ADS)

Cervato, C.; Fils, D.; Bohling, G.; Diver, P.; Greer, D.; Reed, J.; Tang, X.

2006-12-01

The federation of databases is not a new endeavor. Great strides have been made e.g. in the health and astrophysics communities. Reviews of those successes indicate that they have been able to leverage off key cross-community core concepts. In its simplest implementation, a federation of databases with identical base schemas that can be extended to address individual efforts, is relatively easy to accomplish. Efforts of groups like the Open Geospatial Consortium have shown methods to geospatially relate data between different sources. We present here a summary of CHRONOS's (http://www.chronos.org) experience with highly heterogeneous data. Our experience with the federation of very diverse databases shows that the wide variety of encoding options for items like locality, time scale, taxon ID, and other key parameters makes it difficult to effectively join data across them. However, the response to this is not to develop one large, monolithic database, which will suffer growth pains due to social, national, and operational issues, but rather to systematically develop the architecture that will enable cross-resource (database, repository, tool, interface) interaction. CHRONOS has accomplished the major hurdle of federating small IT database efforts with service-oriented and XML-based approaches. The application of easy-to-use procedures that allow groups of all sizes to implement and experiment with searches across various databases and to use externally created tools is vital. We are sharing with the geoinformatics community the difficulties with application frameworks, user authentication, standards compliance, and data storage encountered in setting up web sites and portals for various science initiatives (e.g., ANDRILL, EARTHTIME). The ability to incorporate CHRONOS data, services, and tools into the existing framework of a group is crucial to the development of a model that supports and extends the vitality of the small- to medium-sized research effort that is essential for a vibrant scientific community. This presentation will directly address issues of portal development related to JSR-168 and other portal API's as well as issues related to both federated and local directory-based authentication. The application of service-oriented architecture in connection with ReST-based approaches is vital to facilitate service use by experienced and less experienced information technology groups. Application of these services with XML- based schemas allows for the connection to third party tools such a GIS-based tools and software designed to perform a specific scientific analysis. The connection of all these capabilities into a combined framework based on the standard XHTML Document object model and CSS 2.0 standards used in traditional web development will be demonstrated. CHRONOS also utilizes newer client techniques such as AJAX and cross- domain scripting along with traditional server-side database, application, and web servers. The combination of the various components of this architecture creates an environment based on open and free standards that allows for the discovery, retrieval, and integration of tools and data.

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.

XML under the Hood.

ERIC Educational Resources Information Center

Scharf, David

2002-01-01

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

XML-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.

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

PubMed Central

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

2002-01-01

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

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.

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

Application of Open Source Software by the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Ramirez, P.; Goodale, C. E.; Bui, B.; Chang, G.; Kim, R. M.; Law, E.; Malhotra, S.; Rodriguez, L.; Sadaqathullah, S.; Mattmann, C. A.; Crichton, D. J.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is responsible for the development of an information system to support lunar exploration, decision analysis, and release of lunar data to the public. The data available through the lunar portal is predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). This project has created a gold source of data, models, and tools for lunar explorers to exercise and incorporate into their activities. At Jet Propulsion Laboratory (JPL), we focused on engineering and building the infrastructure to support cataloging, archiving, accessing, and delivery of lunar data. We decided to use a RESTful service-oriented architecture to enable us to abstract from the underlying technology choices and focus on interfaces to be used internally and externally. This decision allowed us to leverage several open source software components and integrate them by either writing a thin REST service layer or relying on the API they provided; the approach chosen was dependent on the targeted consumer of a given interface. We will discuss our varying experience using open source products; namely Apache OODT, Oracle Berkley DB XML, Apache Solr, and Oracle OpenSSO (now named OpenAM). Apache OODT, developed at NASA's Jet Propulsion Laboratory and recently migrated over to Apache, provided the means for ingestion and cataloguing of products within the infrastructure. Its usage was based upon team experience with the project and past benefit received on other projects internal and external to JPL. Berkeley DB XML, distributed by Oracle for both commercial and open source use, was the storage technology chosen for our metadata. This decision was in part based on our use Federal Geographic Data Committee (FGDC) Metadata, which is expressed in XML, and the desire to keep it in its native form and exploit other technologies built on top of XML. Apache Solr, an open source search engine, was used to drive our search interface and as way to store references to metadata and data exposed via REST endpoints. As was the case with Apache OODT there was team experience with this component that helped drive this choice. Lastly, OpenSSO, an open source single sign on service, was used to secure and provide access constraints to our REST based services. For this product there was little past experience but given our service based approach seemed to be a natural fit. Given our exposure to open source we will discuss the tradeoffs and benefits received by the choices made. Moreover, we will dive into the context of how the software packages were used and the impact of their design and extensibility had on the construction of the infrastructure. Finally, we will compare our encounter across open source solutions and attributes that can vary the impression one will get. This comprehensive account of our endeavor should aid others in their assessment and use of open source.

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

The development of MML (Medical Markup Language) version 3.0 as a medical document exchange format for HL7 messages.

PubMed

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

2004-12-01

Medical Markup Language (MML), as a set of standards, has been developed over the last 8 years to allow the exchange of medical data between different medical information providers. MML Version 2.21 used XML as a metalanguage and was announced in 1999. In 2001, MML was updated to Version 2.3, which contained 12 modules. The latest version--Version 3.0--is based on the HL7 Clinical Document Architecture (CDA). During the development of this new version, the structure of MML Version 2.3 was analyzed, subdivided into several categories, and redefined so the information defined in MML could be described in HL7 CDA Level One. As a result of this development, it has become possible to exchange MML Version 3.0 medical documents via HL7 messages.

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.

Multimodal browsing using VoiceXML

NASA Astrophysics Data System (ADS)

Caccia, Giuseppe; Lancini, Rosa C.; Peschiera, Giuseppe

2003-06-01

With the increasing development of devices such as personal computers, WAP and personal digital assistants connected to the World Wide Web, end users feel the need to browse the Internet through multiple modalities. We intend to investigate on how to create a user interface and a service distribution platform granting the user access to the Internet through standard I/O modalities and voice simultaneously. Different architectures are evaluated suggesting the more suitable for each client terminal (PC o WAP). In particular the design of the multimodal usermachine interface considers the synchronization issue between graphical and voice contents.

E-health and healthcare enterprise information system leveraging service-oriented architecture.

PubMed

Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Cheng, Po-Hsun; Lai, Feipei

2012-04-01

To present the successful experiences of an integrated, collaborative, distributed, large-scale enterprise healthcare information system over a wired and wireless infrastructure in National Taiwan University Hospital (NTUH). In order to smoothly and sequentially transfer from the complex relations among the old (legacy) systems to the new-generation enterprise healthcare information system, we adopted the multitier framework based on service-oriented architecture to integrate the heterogeneous systems as well as to interoperate among many other components and multiple databases. We also present mechanisms of a logical layer reusability approach and data (message) exchange flow via Health Level 7 (HL7) middleware, DICOM standard, and the Integrating the Healthcare Enterprise workflow. The architecture and protocols of the NTUH enterprise healthcare information system, especially in the Inpatient Information System (IIS), are discussed in detail. The NTUH Inpatient Healthcare Information System is designed and deployed on service-oriented architecture middleware frameworks. The mechanisms of integration as well as interoperability among the components and the multiple databases apply the HL7 standards for data exchanges, which are embedded in XML formats, and Microsoft .NET Web services to integrate heterogeneous platforms. The preliminary performance of the current operation IIS is evaluated and analyzed to verify the efficiency and effectiveness of the designed architecture; it shows reliability and robustness in the highly demanding traffic environment of NTUH. The newly developed NTUH IIS provides an open and flexible environment not only to share medical information easily among other branch hospitals, but also to reduce the cost of maintenance. The HL7 message standard is widely adopted to cover all data exchanges in the system. All services are independent modules that enable the system to be deployed and configured to the highest degree of flexibility. Furthermore, we can conclude that the multitier Inpatient Healthcare Information System has been designed successfully and in a collaborative manner, based on the index of performance evaluations, central processing unit, and memory utilizations.

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

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

Using architectures for semantic interoperability to create journal clubs for emergency response

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

Powell, James E; Collins, Linn M; Martinez, Mark L B

2009-01-01

In certain types of 'slow burn' emergencies, careful accumulation and evaluation of information can offer a crucial advantage. The SARS outbreak in the first decade of the 21st century was such an event, and ad hoc journal clubs played a critical role in assisting scientific and technical responders in identifying and developing various strategies for halting what could have become a dangerous pandemic. This research-in-progress paper describes a process for leveraging emerging semantic web and digital library architectures and standards to (1) create a focused collection of bibliographic metadata, (2) extract semantic information, (3) convert it to the Resource Descriptionmore » Framework /Extensible Markup Language (RDF/XML), and (4) integrate it so that scientific and technical responders can share and explore critical information in the collections.« less

Instrument Remote Control Application Framework

NASA Technical Reports Server (NTRS)

Ames, Troy; Hostetter, Carl F.

2006-01-01

The Instrument Remote Control (IRC) architecture is a flexible, platform-independent application framework that is well suited for the control and monitoring of remote devices and sensors. IRC enables significant savings in development costs by utilizing extensible Markup Language (XML) descriptions to configure the framework for a specific application. The Instrument Markup Language (IML) is used to describe the commands used by an instrument, the data streams produced, the rules for formatting commands and parsing the data, and the method of communication. Often no custom code is needed to communicate with a new instrument or device. An IRC instance can advertise and publish a description about a device or subscribe to another device's description on a network. This simple capability of dynamically publishing and subscribing to interfaces enables a very flexible, self-adapting architecture for monitoring and control of complex instruments in diverse environments.

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…

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2008-09-01

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

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.

Use of ebRIM-based CSW with sensor observation services for registry and discovery of remote-sensing observations

NASA Astrophysics Data System (ADS)

Chen, Nengcheng; Di, Liping; Yu, Genong; Gong, Jianya; Wei, Yaxing

2009-02-01

Recent advances in Sensor Web geospatial data capture, such as high-resolution in satellite imagery and Web-ready data processing and modeling technologies, have led to the generation of large numbers of datasets from real-time or near real-time observations and measurements. Finding which sensor or data complies with criteria such as specific times, locations, and scales has become a bottleneck for Sensor Web-based applications, especially remote-sensing observations. In this paper, an architecture for use of the integration Sensor Observation Service (SOS) with the Open Geospatial Consortium (OGC) Catalogue Service-Web profile (CSW) is put forward. The architecture consists of a distributed geospatial sensor observation service, a geospatial catalogue service based on the ebXML Registry Information Model (ebRIM), SOS search and registry middleware, and a geospatial sensor portal. The SOS search and registry middleware finds the potential SOS, generating data granule information and inserting the records into CSW. The contents and sequence of the services, the available observations, and the metadata of the observations registry are described. A prototype system is designed and implemented using the service middleware technology and a standard interface and protocol. The feasibility and the response time of registry and retrieval of observations are evaluated using a realistic Earth Observing-1 (EO-1) SOS scenario. Extracting information from SOS requires the same execution time as record generation for CSW. The average data retrieval response time in SOS+CSW mode is 17.6% of that of the SOS-alone mode. The proposed architecture has the more advantages of SOS search and observation data retrieval than the existing sensor Web enabled systems.

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.

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

The neuron classification problem

PubMed Central

Bota, Mihail; Swanson, Larry W.

2007-01-01

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and “Petilla Convention” guidelines, hierarchies, and relations—with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

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.

Some Programs Should Not Run on Laptops - Providing Programmatic Access to Applications Via Web Services

NASA Astrophysics Data System (ADS)

Gupta, V.; Gupta, N.; Gupta, S.; Field, E.; Maechling, P.

2003-12-01

Modern laptop computers, and personal computers, can provide capabilities that are, in many ways, comparable to workstations or departmental servers. However, this doesn't mean we should run all computations on our local computers. We have identified several situations in which it preferable to implement our seismological application programs in a distributed, server-based, computing model. In this model, application programs on the user's laptop, or local computer, invoke programs that run on an organizational server, and the results are returned to the invoking system. Situations in which a server-based architecture may be preferred include: (a) a program is written in a language, or written for an operating environment, that is unsupported on the local computer, (b) software libraries or utilities required to execute a program are not available on the users computer, (c) a computational program is physically too large, or computationally too expensive, to run on a users computer, (d) a user community wants to enforce a consistent method of performing a computation by standardizing on a single implementation of a program, and (e) the computational program may require current information, that is not available to all client computers. Until recently, distributed, server-based, computational capabilities were implemented using client/server architectures. In these architectures, client programs were often written in the same language, and they executed in the same computing environment, as the servers. Recently, a new distributed computational model, called Web Services, has been developed. Web Services are based on Internet standards such as XML, SOAP, WDSL, and UDDI. Web Services offer the promise of platform, and language, independent distributed computing. To investigate this new computational model, and to provide useful services to the SCEC Community, we have implemented several computational and utility programs using a Web Service architecture. We have hosted these Web Services as a part of the SCEC Community Modeling Environment (SCEC/CME) ITR Project (http://www.scec.org/cme). We have implemented Web Services for several of the reasons sited previously. For example, we implemented a FORTRAN-based Earthquake Rupture Forecast (ERF) as a Web Service for use by client computers that don't support a FORTRAN runtime environment. We implemented a Generic Mapping Tool (GMT) Web Service for use by systems that don't have local access to GMT. We implemented a Hazard Map Calculator Web Service to execute Hazard calculations that are too computationally intensive to run on a local system. We implemented a Coordinate Conversion Web Service to enforce a standard and consistent method for converting between UTM and Lat/Lon. Our experience developing these services indicates both strengths and weakness in current Web Service technology. Client programs that utilize Web Services typically need network access, a significant disadvantage at times. Programs with simple input and output parameters were the easiest to implement as Web Services, while programs with complex parameter-types required a significant amount of additional development. We also noted that Web services are very data-oriented, and adapting object-oriented software into the Web Service model proved problematic. Also, the Web Service approach of converting data types into XML format for network transmission has significant inefficiencies for some data sets.

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.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

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.

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

PubMed

Sautter, Guido; Böhm, Klemens; Agosti, Donat

2007-01-01

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

Internet-based data interchange with XML

NASA Astrophysics Data System (ADS)

Fuerst, Karl; Schmidt, Thomas

2000-12-01

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

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.

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.

Methods and apparatus for constructing and implementing a universal extension module for processing objects in a database

NASA Technical Reports Server (NTRS)

Li, Chung-Sheng (Inventor); Smith, John R. (Inventor); Chang, Yuan-Chi (Inventor); Jhingran, Anant D. (Inventor); Padmanabhan, Sriram K. (Inventor); Hsiao, Hui-I (Inventor); Choy, David Mun-Hien (Inventor); Lin, Jy-Jine James (Inventor); Fuh, Gene Y. C. (Inventor); Williams, Robin (Inventor)

2004-01-01

Methods and apparatus for providing a multi-tier object-relational database architecture are disclosed. In one illustrative embodiment of the present invention, a multi-tier database architecture comprises an object-relational database engine as a top tier, one or more domain-specific extension modules as a bottom tier, and one or more universal extension modules as a middle tier. The individual extension modules of the bottom tier operationally connect with the one or more universal extension modules which, themselves, operationally connect with the database engine. The domain-specific extension modules preferably provide such functions as search, index, and retrieval services of images, video, audio, time series, web pages, text, XML, spatial data, etc. The domain-specific extension modules may include one or more IBM DB2 extenders, Oracle data cartridges and/or Informix datablades, although other domain-specific extension modules may be used.

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

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

PubMed

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

2009-03-01

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

Experiences Using a Meta-Data Based Integration Infrastructure

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

Critchlow, T.; Masick, R.; Slezak, T.

1999-07-08

A data warehouse that presents data from many of the genomics community data sources in a consistent, intuitive fashion has long been a goal of bioinformatics. Unfortunately, it is one of the goals that has not yet been achieved. One of the major problems encountered by previous attempts has been the high cost of creating and maintaining a warehouse in a dynamic environment. In this abstract we have outlined a meta-data based approach to integrating data sources that begins to address this problem. We have used this infrastructure to successfully integrate new sources into an existing warehouse in substantially lessmore » time than would have traditionally been required--and the resulting mediators are more maintainable than the traditionally defined ones would have been. In the final paper, we will describe in greater detail both our architecture and our experiences using this framework. In particular, we will outline the new, XML based representation of the meta-data, describe how the mediator generator works, and highlight other potential uses for the meta-data.« less

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

A preliminary architecture for building communication software from traffic captures

NASA Astrophysics Data System (ADS)

Acosta, Jaime C.; Estrada, Pedro

2017-05-01

Security analysts are tasked with identifying and mitigating network service vulnerabilities. A common problem associated with in-depth testing of network protocols is the availability of software that communicates across disparate protocols. Many times, the software required to communicate with these services is not publicly available. Developing this software is a time-consuming undertaking that requires expertise and understanding of the protocol specification. The work described in this paper aims at developing a software package that is capable of automatically creating communication clients by using packet capture (pcap) and TShark dissectors. Currently, our focus is on simple protocols with fixed fields. The methodologies developed as part of this work will extend to other complex protocols such as the Gateway Load Balancing Protocol (GLBP), Port Aggregation Protocol (PAgP), and Open Shortest Path First (OSPF). Thus far, we have architected a modular pipeline for an automatic traffic-based software generator. We start the transformation of captured network traffic by employing TShark to convert packets into a Packet Details Markup Language (PDML) file. The PDML file contains a parsed, textual, representation of the packet data. Then, we extract field data, types, along with inter and intra-packet dependencies. This information is then utilized to construct an XML file that encompasses the protocol state machine and field vocabulary. Finally, this XML is converted into executable code. Using our methodology, and as a starting point, we have succeeded in automatically generating software that communicates with other hosts using an automatically generated Internet Control Message Protocol (ICMP) client program.

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

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

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.

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

PubMed

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

2002-01-01

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

The XBabelPhish MAGE-ML and XML translator.

PubMed

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

2008-01-18

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

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…

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

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Design, implementation, use, and preliminary evaluation of SEBASTIAN, a standards-based Web service for clinical decision support.

PubMed

Kawamoto, Kensaku; Lobach, David F

2005-01-01

Despite their demonstrated ability to improve care quality, clinical decision support systems are not widely used. In part, this limited use is due to the difficulty of sharing medical knowledge in a machine-executable format. To address this problem, we developed a decision support Web service known as SEBASTIAN. In SEBASTIAN, individual knowledge modules define the data requirements for assessing a patient, the conclusions that can be drawn using that data, and instructions on how to generate those conclusions. Using standards-based XML messages transmitted over HTTP, client decision support applications provide patient data to SEBASTIAN and receive patient-specific assessments and recommendations. SEBASTIAN has been used to implement four distinct decision support systems; an architectural overview is provided for one of these systems. Preliminary assessments indicate that SEBASTIAN fulfills all original design objectives, including the re-use of executable medical knowledge across diverse applications and care settings, the straightforward authoring of knowledge modules, and use of the framework to implement decision support applications with significant clinical utility.

Multi-Disciplinary Analysis for Future Launch Systems Using NASA's Advanced Engineering Environment (AEE)

NASA Technical Reports Server (NTRS)

Monell, D.; Mathias, D.; Reuther, J.; Garn, M.

2003-01-01

A new engineering environment constructed for the purposes of analyzing and designing Reusable Launch Vehicles (RLVs) is presented. The new environment has been developed to allow NASA to perform independent analysis and design of emerging RLV architectures and technologies. The new Advanced Engineering Environment (AEE) is both collaborative and distributed. It facilitates integration of the analyses by both vehicle performance disciplines and life-cycle disciplines. Current performance disciplines supported include: weights and sizing, aerodynamics, trajectories, propulsion, structural loads, and CAD-based geometries. Current life-cycle disciplines supported include: DDT&E cost, production costs, operations costs, flight rates, safety and reliability, and system economics. Involving six NASA centers (ARC, LaRC, MSFC, KSC, GRC and JSC), AEE has been tailored to serve as a web-accessed agency-wide source for all of NASA's future launch vehicle systems engineering functions. Thus, it is configured to facilitate (a) data management, (b) automated tool/process integration and execution, and (c) data visualization and presentation. The core components of the integrated framework are a customized PTC Windchill product data management server, a set of RLV analysis and design tools integrated using Phoenix Integration's Model Center, and an XML-based data capture and transfer protocol. The AEE system has seen production use during the Initial Architecture and Technology Review for the NASA 2nd Generation RLV program, and it continues to undergo development and enhancements in support of its current main customer, the NASA Next Generation Launch Technology (NGLT) program.

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.

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

A scalable architecture for extracting, aligning, linking, and visualizing multi-Int data

NASA Astrophysics Data System (ADS)

Knoblock, Craig A.; Szekely, Pedro

2015-05-01

An analyst today has a tremendous amount of data available, but each of the various data sources typically exists in their own silos, so an analyst has limited ability to see an integrated view of the data and has little or no access to contextual information that could help in understanding the data. We have developed the Domain-Insight Graph (DIG) system, an innovative architecture for extracting, aligning, linking, and visualizing massive amounts of domain-specific content from unstructured sources. Under the DARPA Memex program we have already successfully applied this architecture to multiple application domains, including the enormous international problem of human trafficking, where we extracted, aligned and linked data from 50 million online Web pages. DIG builds on our Karma data integration toolkit, which makes it easy to rapidly integrate structured data from a variety of sources, including databases, spreadsheets, XML, JSON, and Web services. The ability to integrate Web services allows Karma to pull in live data from the various social media sites, such as Twitter, Instagram, and OpenStreetMaps. DIG then indexes the integrated data and provides an easy to use interface for query, visualization, and analysis.

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.

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.

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

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.

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.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

The Mars Relay Operations Service (MaROS) is designed to provide planning and analysis tools in support of ongoing Mars Network relay operations. Strategic relay planning requires coordination between lander and orbiter mission ground data system (GDS) teams to schedule and execute relay communications passes. MaROS centralizes this process, correlating all data relevant to relay coordination to provide a cohesive picture of the relay state. Service users interact with the system through thin-layer command line and web user interface client applications. Users provide and utilize data such as lander view periods of orbiters, Deep Space Network (DSN) antenna tracks, and reports of relay pass performance. Users upload and download relevant relay data via formally defined and documented file structures including some described in Extensible Markup Language (XML). Clients interface with the system via an http-based Representational State Transfer (ReST) pattern using Javascript Object Notation (JSON) formats. This paper will provide a general overview of the service architecture and detail the software interfaces and considerations for interface design.

A web application to support telemedicine services in Brazil.

PubMed

Barbosa, Ana Karina P; de A Novaes, Magdala; de Vasconcelos, Alexandre M L

2003-01-01

This paper describes a system that has been developed to support Telemedicine activities in Brazil, a country that has serious problems in the delivery of health services. The system is a part of the broader Tele-health Project that has been developed to make health services more accessible to the low-income population in the northeast region. The HealthNet system is based upon a pilot area that uses fetal and pediatric cardiology. This article describes both the system's conceptual model, including the tele-diagnosis and second medical opinion services, as well as its architecture and development stages. The system model describes both collaborating tools used asynchronously, such as discussion forums, and synchronous tools, such as videoconference services. Web and free-of-charge tools are utilized for implementation, such as Java and MySQL database. Furthermore, an interface with Electronic Patient Record (EPR) systems using Extended Markup Language (XML) technology is also proposed. Finally, considerations concerning the development and implementation process are presented.

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

Graf, Norman A.; /SLAC

Maximizing the physics performance of detectors being designed for the International Linear Collider, while remaining sensitive to cost constraints, requires a powerful, efficient, and flexible simulation, reconstruction and analysis environment to study the capabilities of a large number of different detector designs. The preparation of Letters Of Intent for the International Linear Collider involved the detailed study of dozens of detector options, layouts and readout technologies; the final physics benchmarking studies required the reconstruction and analysis of hundreds of millions of events. We describe the Java-based software toolkit (org.lcsim) which was used for full event reconstruction and analysis. The componentsmore » are fully modular and are available for tasks from digitization of tracking detector signals through to cluster finding, pattern recognition, track-fitting, calorimeter clustering, individual particle reconstruction, jet-finding, and analysis. The detector is defined by the same xml input files used for the detector response simulation, ensuring the simulation and reconstruction geometries are always commensurate by construction. We discuss the architecture as well as the performance.« less

Towards a distributed information architecture for avionics data

NASA Technical Reports Server (NTRS)

Mattmann, Chris; Freeborn, Dana; Crichton, Dan

2003-01-01

Avionics data at the National Aeronautics and Space Administration's (NASA) Jet Propulsion Laboratory (JPL consists of distributed, unmanaged, and heterogeneous information that is hard for flight system design engineers to find and use on new NASA/JPL missions. The development of a systematic approach for capturing, accessing and sharing avionics data critical to the support of NASA/JPL missions and projects is required. We propose a general information architecture for managing the existing distributed avionics data sources and a method for querying and retrieving avionics data using the Object Oriented Data Technology (OODT) framework. OODT uses XML messaging infrastructure that profiles data products and their locations using the ISO-11179 data model for describing data products. Queries against a common data dictionary (which implements the ISO model) are translated to domain dependent source data models, and distributed data products are returned asynchronously through the OODT middleware. Further work will include the ability to 'plug and play' new manufacturer data sources, which are distributed at avionics component manufacturer locations throughout the United States.

Applying Sensor Web Technology to Marine Sensor Data

NASA Astrophysics Data System (ADS)

Jirka, Simon; del Rio, Joaquin; Mihai Toma, Daniel; Nüst, Daniel; Stasch, Christoph; Delory, Eric

2015-04-01

In this contribution we present two activities illustrating how Sensor Web technology helps to enable a flexible and interoperable sharing of marine observation data based on standards. An important foundation is the Sensor Web Architecture developed by the European FP7 project NeXOS (Next generation Low-Cost Multifunctional Web Enabled Ocean Sensor Systems Empowering Marine, Maritime and Fisheries Management). This architecture relies on the Open Geospatial Consortium's (OGC) Sensor Web Enablement (SWE) framework. It is an exemplary solution for facilitating the interoperable exchange of marine observation data within and between (research) organisations. The architecture addresses a series of functional and non-functional requirements which are fulfilled through different types of OGC SWE components. The diverse functionalities offered by the NeXOS Sensor Web architecture are shown in the following overview: - Pull-based observation data download: This is achieved through the OGC Sensor Observation Service (SOS) 2.0 interface standard. - Push-based delivery of observation data to allow users the subscription to new measurements that are relevant for them: For this purpose there are currently several specification activities under evaluation (e.g. OGC Sensor Event Service, OGC Publish/Subscribe Standards Working Group). - (Web-based) visualisation of marine observation data: Implemented through SOS client applications. - Configuration and controlling of sensor devices: This is ensured through the OGC Sensor Planning Service 2.0 interface. - Bridging between sensors/data loggers and Sensor Web components: For this purpose several components such as the "Smart Electronic Interface for Sensor Interoperability" (SEISI) concept are developed; this is complemented by a more lightweight SOS extension (e.g. based on the W3C Efficient XML Interchange (EXI) format). To further advance this architecture, there is on-going work to develop dedicated profiles of selected OGC SWE specifications that provide stricter guidance how these standards shall be applied to marine data (e.g. SensorML 2.0 profiles stating which metadata elements are mandatory building upon the ESONET Sensor Registry developments, etc.). Within the NeXOS project the presented architecture is implemented as a set of open source components. These implementations can be re-used by all interested scientists and data providers needing tools for publishing or consuming oceanographic sensor data. In further projects such as the European project FixO3 (Fixed-point Open Ocean Observatories), these software development activities are complemented with additional efforts to provide guidance how Sensor Web technology can be applied in an efficient manner. This way, not only software components are made available but also documentation and information resources that help to understand which types of Sensor Web deployments are best suited to fulfil different types of user requirements.

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

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.

THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA

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

Devarakonda, Ranjeet; Shrestha, Biva; Palanisamy, Giri

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

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.

Data Model Management for Space Information Systems

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Daniel J.; Ramirez, Paul; Mattmann, chris

2006-01-01

The Reference Architecture for Space Information Management (RASIM) suggests the separation of the data model from software components to promote the development of flexible information management systems. RASIM allows the data model to evolve independently from the software components and results in a robust implementation that remains viable as the domain changes. However, the development and management of data models within RASIM are difficult and time consuming tasks involving the choice of a notation, the capture of the model, its validation for consistency, and the export of the model for implementation. Current limitations to this approach include the lack of ability to capture comprehensive domain knowledge, the loss of significant modeling information during implementation, the lack of model visualization and documentation capabilities, and exports being limited to one or two schema types. The advent of the Semantic Web and its demand for sophisticated data models has addressed this situation by providing a new level of data model management in the form of ontology tools. In this paper we describe the use of a representative ontology tool to capture and manage a data model for a space information system. The resulting ontology is implementation independent. Novel on-line visualization and documentation capabilities are available automatically, and the ability to export to various schemas can be added through tool plug-ins. In addition, the ingestion of data instances into the ontology allows validation of the ontology and results in a domain knowledge base. Semantic browsers are easily configured for the knowledge base. For example the export of the knowledge base to RDF/XML and RDFS/XML and the use of open source metadata browsers provide ready-made user interfaces that support both text- and facet-based search. This paper will present the Planetary Data System (PDS) data model as a use case and describe the import of the data model into an ontology tool. We will also describe the current effort to provide interoperability with the European Space Agency (ESA)/Planetary Science Archive (PSA) which is critically dependent on a common data model.

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.

NOAO observing proposal processing system

NASA Astrophysics Data System (ADS)

Bell, David J.; Gasson, David; Hartman, Mia

2002-12-01

Since going electronic in 1994, NOAO has continued to refine and enhance its observing proposal handling system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form or via Gemini's downloadable Phase-I Tool. NOAO staff can use online interfaces for administrative tasks, technical reviews, telescope scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available online. The system, now known as ANDES, is designed as a thin-client architecture (web pages are now used for almost all database functions) built using open source tools (FreeBSD, Apache, MySQL, Perl, PHP) to process descriptively-marked (LaTeX, XML) proposal documents.

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more

PubMed Central

Fumoto, Masaki; Miyazaki, Satoru; Sugawara, Hideaki

2002-01-01

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/. PMID:11752256

"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

Progress on an implementation of MIFlowCyt in XML

NASA Astrophysics Data System (ADS)

Leif, Robert C.; Leif, Stephanie H.

2015-03-01

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

Application of XML to Journal Table Archiving

NASA Astrophysics Data System (ADS)

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

1998-12-01

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

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.

GEO Label Web Services for Dynamic and Effective Communication of Geospatial Metadata Quality

NASA Astrophysics Data System (ADS)

Lush, Victoria; Nüst, Daniel; Bastin, Lucy; Masó, Joan; Lumsden, Jo

2014-05-01

We present demonstrations of the GEO label Web services and their integration into a prototype extension of the GEOSS portal (http://scgeoviqua.sapienzaconsulting.com/web/guest/geo_home), the GMU portal (http://gis.csiss.gmu.edu/GADMFS/) and a GeoNetwork catalog application (http://uncertdata.aston.ac.uk:8080/geonetwork/srv/eng/main.home). The GEO label is designed to communicate, and facilitate interrogation of, geospatial quality information with a view to supporting efficient and effective dataset selection on the basis of quality, trustworthiness and fitness for use. The GEO label which we propose was developed and evaluated according to a user-centred design (UCD) approach in order to maximise the likelihood of user acceptance once deployed. The resulting label is dynamically generated from producer metadata in ISO or FDGC format, and incorporates user feedback on dataset usage, ratings and discovered issues, in order to supply a highly informative summary of metadata completeness and quality. The label was easily incorporated into a community portal as part of the GEO Architecture Implementation Programme (AIP-6) and has been successfully integrated into a prototype extension of the GEOSS portal, as well as the popular metadata catalog and editor, GeoNetwork. The design of the GEO label was based on 4 user studies conducted to: (1) elicit initial user requirements; (2) investigate initial user views on the concept of a GEO label and its potential role; (3) evaluate prototype label visualizations; and (4) evaluate and validate physical GEO label prototypes. The results of these studies indicated that users and producers support the concept of a label with drill-down interrogation facility, combining eight geospatial data informational aspects, namely: producer profile, producer comments, lineage information, standards compliance, quality information, user feedback, expert reviews, and citations information. These are delivered as eight facets of a wheel-like label, which are coloured according to metadata availability and are clickable to allow a user to engage with the original metadata and explore specific aspects in more detail. To support this graphical representation and allow for wider deployment architectures we have implemented two Web services, a PHP and a Java implementation, that generate GEO label representations by combining producer metadata (from standard catalogues or other published locations) with structured user feedback. Both services accept encoded URLs of publicly available metadata documents or metadata XML files as HTTP POST and GET requests and apply XPath and XSLT mappings to transform producer and feedback XML documents into clickable SVG GEO label representations. The label and services are underpinned by two XML-based quality models. The first is a producer model that extends ISO 19115 and 19157 to allow fuller citation of reference data, presentation of pixel- and dataset- level statistical quality information, and encoding of 'traceability' information on the lineage of an actual quality assessment. The second is a user quality model (realised as a feedback server and client) which allows reporting and query of ratings, usage reports, citations, comments and other domain knowledge. Both services are Open Source and are available on GitHub at https://github.com/lushv/geolabel-service and https://github.com/52North/GEO-label-java. The functionality of these services can be tested using our GEO label generation demos, available online at http://www.geolabel.net/demo.html and http://geoviqua.dev.52north.org/glbservice/index.jsf.

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

Standardized Procedure Content And Data Structure Based On Human Factors Requirements For Computer-Based Procedures

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

Bly, Aaron; Oxstrand, Johanna; Le Blanc, Katya L

2015-02-01

Most activities that involve human interaction with systems in a nuclear power plant are guided by procedures. Traditionally, the use of procedures has been a paper-based process that supports safe operation of the nuclear power industry. However, the nuclear industry is constantly trying to find ways to decrease the human error rate, especially the human errors associated with procedure use. Advances in digital technology make computer-based procedures (CBPs) a valid option that provides further enhancement of safety by improving human performance related to procedure use. The transition from paper-based procedures (PBPs) to CBPs creates a need for a computer-based proceduremore » system (CBPS). A CBPS needs to have the ability to perform logical operations in order to adjust to the inputs received from either users or real time data from plant status databases. Without the ability for logical operations the procedure is just an electronic copy of the paper-based procedure. In order to provide the CBPS with the information it needs to display the procedure steps to the user, special care is needed in the format used to deliver all data and instructions to create the steps. The procedure should be broken down into basic elements and formatted in a standard method for the CBPS. One way to build the underlying data architecture is to use an Extensible Markup Language (XML) schema, which utilizes basic elements to build each step in the smart procedure. The attributes of each step will determine the type of functionality that the system will generate for that step. The CBPS will provide the context for the step to deliver referential information, request a decision, or accept input from the user. The XML schema needs to provide all data necessary for the system to accurately perform each step without the need for the procedure writer to reprogram the CBPS. The research team at the Idaho National Laboratory has developed a prototype CBPS for field workers as well as the underlying data structure for such CBPS. The objective of the research effort is to develop guidance on how to design both the user interface and the underlying schema. This paper will describe the result and insights gained from the research activities conducted to date.« less

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…

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.

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/.

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.

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.

WMS Server 2.0

NASA Technical Reports Server (NTRS)

Plesea, Lucian; Wood, James F.

2012-01-01

This software is a simple, yet flexible server of raster map products, compliant with the Open Geospatial Consortium (OGC) Web Map Service (WMS) 1.1.1 protocol. The server is a full implementation of the OGC WMS 1.1.1 as a fastCGI client and using Geospatial Data Abstraction Library (GDAL) for data access. The server can operate in a proxy mode, where all or part of the WMS requests are done on a back server. The server has explicit support for a colocated tiled WMS, including rapid response of black (no-data) requests. It generates JPEG and PNG images, including 16-bit PNG. The GDAL back-end support allows great flexibility on the data access. The server is a port to a Linux/GDAL platform from the original IRIX/IL platform. It is simpler to configure and use, and depending on the storage format used, it has better performance than other available implementations. The WMS server 2.0 is a high-performance WMS implementation due to the fastCGI architecture. The use of GDAL data back end allows for great flexibility. The configuration is relatively simple, based on a single XML file. It provides scaling and cropping, as well as blending of multiple layers based on layer transparency.

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

Weng, Y. H.; Sun, F. S.

2014-12-01

A web-based field data management system has been designed and developed to allow field geologists to store, organize, manage, and share field data online. System requirements were analyzed and clearly defined first regarding what data are to be stored, who the potential users are, and what system functions are needed in order to deliver the right data in the right way to the right user. A 3-tiered architecture was adopted to create this secure, scalable system that consists of a web browser at the front end while a database at the back end and a functional logic server in the middle. Specifically, HTML, CSS, and JavaScript were used to implement the user interface in the front-end tier, the Apache web server runs PHP scripts, and MySQL to server is used for the back-end database. The system accepts various types of field information, including image, audio, video, numeric, and text. It allows users to select data and populate them on either Google Earth or Google Maps for the examination of the spatial relations. It also makes the sharing of field data easy by converting them into XML format that is both human-readable and machine-readable, and thus ready for reuse.

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.

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)

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.

CISN Display - Reliable Delivery of Real-time Earthquake Information, Including Rapid Notification and ShakeMap to Critical End Users

NASA Astrophysics Data System (ADS)

Rico, H.; Hauksson, E.; Thomas, E.; Friberg, P.; Given, D.

2002-12-01

The California Integrated Seismic Network (CISN) Display is part of a Web-enabled earthquake notification system alerting users in near real-time of seismicity, and also valuable geophysical information following a large earthquake. It will replace the Caltech/USGS Broadcast of Earthquakes (CUBE) and Rapid Earthquake Data Integration (REDI) Display as the principal means of delivering graphical earthquake information to users at emergency operations centers, and other organizations. Features distinguishing the CISN Display from other GUI tools are a state-full client/server relationship, a scalable message format supporting automated hyperlink creation, and a configurable platform-independent client with a GIS mapping tool; supporting the decision-making activities of critical users. The CISN Display is the front-end of a client/server architecture known as the QuakeWatch system. It is comprised of the CISN Display (and other potential clients), message queues, server, server "feeder" modules, and messaging middleware, schema and generators. It is written in Java, making it platform-independent, and offering the latest in Internet technologies. QuakeWatch's object-oriented design allows components to be easily upgraded through a well-defined set of application programming interfaces (APIs). Central to the CISN Display's role as a gateway to other earthquake products is its comprehensive XML-schema. The message model starts with the CUBE message format, but extends it by provisioning additional attributes for currently available products, and those yet to be considered. The supporting metadata in the XML-message provides the data necessary for the client to create a hyperlink and associate it with a unique event ID. Earthquake products deliverable to the CISN Display are ShakeMap, Ground Displacement, Focal Mechanisms, Rapid Notifications, OES Reports, and Earthquake Commentaries. Leveraging the power of the XML-format, the CISN Display provides prompt access to earthquake information on the Web. The links are automatically created when product generators deliver CUBE formatted packets to a Quake Data Distribution System (QDDS) hub (new distribution methods may be used later). The "feeder" modules tap into the QDDS hub and convert the packets into XML-messages. These messages are forwarded to message queues, and then distributed to clients where URLs are dynamically created for these products and linked to events on the CISN Display map. The products may be downloaded out-of-band; and with the inclusion of a GIS mapping tool users can plot organizational assets on the CISN Display map and overlay them against key spectral data, such as ground accelerations. This gives Emergency Response Managers information useful in allocating limited personnel and resources after a major event. At the heart of the system's robustness is a well-established and reliable set of communication protocols for best-effort delivery of data. For critical users a Common Object Request Broker Architecture (CORBA) state-full connection is used via a dedicated signaling channel. The system employs several CORBA methods that alert users of changes in the link status. Loss of connectivity triggers a strategy that attempts to reconnect through various physical and logical paths. Thus, by building on past application successes and proven Internet advances the CISN Display targets a specific audience by providing enhancements previously not available from other applications.

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.

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

PubMed Central

Kusber, W.-H.; Tschöpe, O.; Güntsch, A.; Berendsohn, W. G.

2017-01-01

Abstract Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an important pathway of research documentation and data quality control is broken. In order to create an online annotation system, we analysed, modeled and adapted traditional specimen annotation workflows. The AnnoSys system accesses collection data from either conventional web resources or the Biological Collection Access Service (BioCASe) and accepts XML-based data standards like ABCD or DarwinCore. It comprises a searchable annotation data repository, a user interface, and a subscription based message system. We describe the main components of AnnoSys and its current and planned interoperability with biodiversity data portals and networks. Details are given on the underlying architectural model, which implements the W3C OpenAnnotation model and allows the adaptation of AnnoSys to different problem domains. Advantages and disadvantages of different digital annotation and feedback approaches are discussed. For the biodiversity domain, AnnoSys proposes best practice procedures for digital annotations of complex records. Database URL: https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys PMID:28365735

An introduction to the Semantic Web for health sciences librarians.

PubMed

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-04-01

The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

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).

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

PubMed

Klann, Jeffrey G; Murphy, Shawn N

2013-04-19

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

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

PubMed Central

Murphy, Shawn N

2013-01-01

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

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.

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...

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.

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.

Conceptual Design of Simulation Models in an Early Development Phase of Lunar Spacecraft Simulator Using SMP2 Standard

NASA Astrophysics Data System (ADS)

Lee, Hoon Hee; Koo, Cheol Hea; Moon, Sung Tae; Han, Sang Hyuck; Ju, Gwang Hyeok

2013-08-01

The conceptual study for Korean lunar orbiter/lander prototype has been performed in Korea Aerospace Research Institute (KARI). Across diverse space programs around European countries, a variety of simulation application has been developed using SMP2 (Simulation Modelling Platform) standard related to portability and reuse of simulation models by various model users. KARI has not only first-hand experience of a development of SMP compatible simulation environment but also an ongoing study to apply the SMP2 development process of simulation model to a simulator development project for lunar missions. KARI has tried to extend the coverage of the development domain based on SMP2 standard across the whole simulation model life-cycle from software design to its validation through a lunar exploration project. Figure. 1 shows a snapshot from a visualization tool for the simulation of lunar lander motion. In reality, a demonstrator prototype on the right-hand side of image was made and tested in 2012. In an early phase of simulator development prior to a kick-off start in the near future, targeted hardware to be modelled has been investigated and indentified at the end of 2012. The architectural breakdown of the lunar simulator at system level was performed and the architecture with a hierarchical tree of models from the system to parts at lower level has been established. Finally, SMP Documents such as Catalogue, Assembly, Schedule and so on were converted using a XML(eXtensible Mark-up Language) converter. To obtain benefits of the suggested approaches and design mechanisms in SMP2 standard as far as possible, the object-oriented and component-based design concepts were strictly chosen throughout a whole model development process.

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

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.

Implementation of workflow engine technology to deliver basic clinical decision support functionality.

PubMed

Huser, Vojtech; Rasmussen, Luke V; Oberg, Ryan; Starren, Justin B

2011-04-10

Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform.

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.

Tsunami.gov: NOAA's Tsunami Information Portal

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Domain Modeling and Application Development of an Archetype- and XML-based EHRS. Practical Experiences and Lessons Learnt.

PubMed

Kropf, Stefan; Chalopin, Claire; Lindner, Dirk; Denecke, Kerstin

2017-06-28

Access to patient data within the hospital or between hospitals is still problematic since a variety of information systems is in use applying different vendor specific terminologies and underlying knowledge models. Beyond, the development of electronic health record systems (EHRSs) is time and resource consuming. Thus, there is a substantial need for a development strategy of standardized EHRSs. We are applying a reuse-oriented process model and demonstrate its feasibility and realization on a practical medical use case, which is an EHRS holding all relevant data arising in the context of treatment of tumors of the sella region. In this paper, we describe the development process and our practical experiences. Requirements towards the development of the EHRS were collected by interviews with a neurosurgeon and patient data analysis. For modelling of patient data, we selected openEHR as standard and exploited the software tools provided by the openEHR foundation. The patient information model forms the core of the development process, which comprises the EHR generation and the implementation of an EHRS architecture. Moreover, a reuse-oriented process model from the business domain was adapted to the development of the EHRS. The reuse-oriented process model is a model for a suitable abstraction of both, modeling and development of an EHR centralized EHRS. The information modeling process resulted in 18 archetypes that were aggregated in a template and built the boilerplate of the model driven development. The EHRs and the EHRS were developed by openEHR and W3C standards, tightly supported by well-established XML techniques. The GUI of the final EHRS integrates and visualizes information from various examinations, medical reports, findings and laboratory test results. We conclude that the development of a standardized overarching EHR and an EHRS is feasible using openEHR and W3C standards, enabling a high degree of semantic interoperability. The standardized representation visualizes data and can in this way support the decision process of clinicians.

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

NASA Astrophysics Data System (ADS)

Neuhauser, D. S.; Zuzlewski, S.; Lombard, P. N.; Allen, R. M.

2013-12-01

The Northern California Earthquake Data Center (NCEDC) provides data archive and distribution services for seismological and geophysical data sets that encompass northern California. The NCEDC is enhancing its ability to deliver rapid information through Web Services. NCEDC Web Services use well-established web server and client protocols and REST software architecture to allow users to easily make queries using web browsers or simple program interfaces and to receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, simple text, or MiniSEED depending on the service and selected output format. The NCEDC offers the following web services that are compliant with the International Federation of Digital Seismograph Networks (FDSN) web services specifications: (1) fdsn-dataselect: time series data delivered in MiniSEED format, (2) fdsn-station: station and channel metadata and time series availability delivered in StationXML format, (3) fdsn-event: earthquake event information delivered in QuakeML format. In addition, the NCEDC offers the the following IRIS-compatible web services: (1) sacpz: provide channel gains, poles, and zeros in SAC format, (2) resp: provide channel response information in RESP format, (3) dataless: provide station and channel metadata in Dataless SEED format. The NCEDC is also developing a web service to deliver timeseries from pre-assembled event waveform gathers. The NCEDC has waveform gathers for ~750,000 northern and central California events from 1984 to the present, many of which were created by the USGS NCSN prior to the establishment of the joint NCSS (Northern California Seismic System). We are currently adding waveforms to these older event gathers with time series from the UCB networks and other networks with waveforms archived at the NCEDC, and ensuring that the waveform for each channel in the event gathers have the highest quality waveform from the archive.

Communication and re-use of chemical information in bioscience

PubMed Central

Murray-Rust, Peter; Mitchell, John BO; Rzepa, Henry S

2005-01-01

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective. PMID:16026614

Automating Disk Forensic Processing with SleuthKit, XML and Python

DTIC Science & Technology

2009-05-01

1 Automating Disk Forensic Processing with SleuthKit, XML and Python Simson L. Garfinkel Abstract We have developed a program called fiwalk which...files themselves. We show how it is relatively simple to create automated disk forensic applications using a Python module we have written that reads...software that the portable device may contain. Keywords: Computer Forensics; XML; Sleuth Kit; Python I. INTRODUCTION In recent years we have found many

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

NASA Tech Briefs, October 2008

NASA Technical Reports Server (NTRS)

2008-01-01

Topics covered include: Control Architecture for Robotic Agent Command and Sensing; Algorithm for Wavefront Sensing Using an Extended Scene; CO2 Sensors Based on Nanocrystalline SnO2 Doped with CuO; Improved Airborne System for Sensing Wildfires; VHF Wide-Band, Dual-Polarization Microstrip-Patch Antenna; Onboard Data Processor for Change-Detection Radar Imaging; Using LDPC Code Constraints to Aid Recovery of Symbol Timing; System for Measuring Flexing of a Large Spaceborne Structure; Integrated Formation Optical Communication and Estimation System; Making Superconducting Welds between Superconducting Wires; Method for Thermal Spraying of Coatings Using Resonant-Pulsed Combustion; Coating Reduces Ice Adhesion; Hybrid Multifoil Aerogel Thermal Insulation; SHINE Virtual Machine Model for In-flight Updates of Critical Mission Software; Mars Image Collection Mosaic Builder; Providing Internet Access to High-Resolution Mars Images; Providing Internet Access to High-Resolution Lunar Images; Expressions Module for the Satellite Orbit Analysis Program Virtual Satellite; Small-Body Extensions for the Satellite Orbit Analysis Program (SOAP); Scripting Module for the Satellite Orbit Analysis Program (SOAP); XML-Based SHINE Knowledge Base Interchange Language; Core Technical Capability Laboratory Management System; MRO SOW Daily Script; Tool for Inspecting Alignment of Twinaxial Connectors; An ATP System for Deep-Space Optical Communication; Polar Traverse Rover Instrument; Expert System Control of Plant Growth in an Enclosed Space; Detecting Phycocyanin-Pigmented Microbes in Reflected Light; DMAC and NMP as Electrolyte Additives for Li-Ion Cells; Mass Spectrometer Containing Multiple Fixed Collectors; Waveguide Harmonic Generator for the SIM; Whispering Gallery Mode Resonator with Orthogonally Reconfigurable Filter Function; Stable Calibration of Raman Lidar Water-Vapor Measurements; Bimaterial Thermal Compensators for WGM Resonators; Root Source Analysis/ValuStream[Trade Mark] - A Methodology for Identifying and Managing Risks; Ensemble: an Architecture for Mission-Operations Software; Object Recognition Using Feature-and Color-Based Methods; On-Orbit Multi-Field Wavefront Control with a Kalman Filter; and The Interplanetary Overlay Networking Protocol Accelerator.

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

DTIC Science & Technology

2010-03-01

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

XML 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.

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

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

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

FAIMS Mobile: Flexible, open-source software for field research

NASA Astrophysics Data System (ADS)

Ballsun-Stanton, Brian; Ross, Shawn A.; Sobotkova, Adela; Crook, Penny

2018-01-01

FAIMS Mobile is a native Android application supported by an Ubuntu server facilitating human-mediated field research across disciplines. It consists of 'core' Java and Ruby software providing a platform for data capture, which can be deeply customised using 'definition packets' consisting of XML documents (data schema and UI) and Beanshell scripts (automation). Definition packets can also be generated using an XML-based domain-specific language, making customisation easier. FAIMS Mobile includes features allowing rich and efficient data capture tailored to the needs of fieldwork. It also promotes synthetic research and improves transparency and reproducibility through the production of comprehensive datasets that can be mapped to vocabularies or ontologies as they are created.

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.

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

Towards computerizing intensive care sedation guidelines: design of a rule-based architecture for automated execution of clinical guidelines

PubMed Central

2010-01-01

Background Computerized ICUs rely on software services to convey the medical condition of their patients as well as assisting the staff in taking treatment decisions. Such services are useful for following clinical guidelines quickly and accurately. However, the development of services is often time-consuming and error-prone. Consequently, many care-related activities are still conducted based on manually constructed guidelines. These are often ambiguous, which leads to unnecessary variations in treatments and costs. The goal of this paper is to present a semi-automatic verification and translation framework capable of turning manually constructed diagrams into ready-to-use programs. This framework combines the strengths of the manual and service-oriented approaches while decreasing their disadvantages. The aim is to close the gap in communication between the IT and the medical domain. This leads to a less time-consuming and error-prone development phase and a shorter clinical evaluation phase. Methods A framework is proposed that semi-automatically translates a clinical guideline, expressed as an XML-based flow chart, into a Drools Rule Flow by employing semantic technologies such as ontologies and SWRL. An overview of the architecture is given and all the technology choices are thoroughly motivated. Finally, it is shown how this framework can be integrated into a service-oriented architecture (SOA). Results The applicability of the Drools Rule language to express clinical guidelines is evaluated by translating an example guideline, namely the sedation protocol used for the anaesthetization of patients, to a Drools Rule Flow and executing and deploying this Rule-based application as a part of a SOA. The results show that the performance of Drools is comparable to other technologies such as Web Services and increases with the number of decision nodes present in the Rule Flow. Most delays are introduced by loading the Rule Flows. Conclusions The framework is an effective solution for computerizing clinical guidelines as it allows for quick development, evaluation and human-readable visualization of the Rules and has a good performance. By monitoring the parameters of the patient to automatically detect exceptional situations and problems and by notifying the medical staff of tasks that need to be performed, the computerized sedation guideline improves the execution of the guideline. PMID:20082700

Towards computerizing intensive care sedation guidelines: design of a rule-based architecture for automated execution of clinical guidelines.

PubMed

Ongenae, Femke; De Backere, Femke; Steurbaut, Kristof; Colpaert, Kirsten; Kerckhove, Wannes; Decruyenaere, Johan; De Turck, Filip

2010-01-18

Computerized ICUs rely on software services to convey the medical condition of their patients as well as assisting the staff in taking treatment decisions. Such services are useful for following clinical guidelines quickly and accurately. However, the development of services is often time-consuming and error-prone. Consequently, many care-related activities are still conducted based on manually constructed guidelines. These are often ambiguous, which leads to unnecessary variations in treatments and costs.The goal of this paper is to present a semi-automatic verification and translation framework capable of turning manually constructed diagrams into ready-to-use programs. This framework combines the strengths of the manual and service-oriented approaches while decreasing their disadvantages. The aim is to close the gap in communication between the IT and the medical domain. This leads to a less time-consuming and error-prone development phase and a shorter clinical evaluation phase. A framework is proposed that semi-automatically translates a clinical guideline, expressed as an XML-based flow chart, into a Drools Rule Flow by employing semantic technologies such as ontologies and SWRL. An overview of the architecture is given and all the technology choices are thoroughly motivated. Finally, it is shown how this framework can be integrated into a service-oriented architecture (SOA). The applicability of the Drools Rule language to express clinical guidelines is evaluated by translating an example guideline, namely the sedation protocol used for the anaesthetization of patients, to a Drools Rule Flow and executing and deploying this Rule-based application as a part of a SOA. The results show that the performance of Drools is comparable to other technologies such as Web Services and increases with the number of decision nodes present in the Rule Flow. Most delays are introduced by loading the Rule Flows. The framework is an effective solution for computerizing clinical guidelines as it allows for quick development, evaluation and human-readable visualization of the Rules and has a good performance. By monitoring the parameters of the patient to automatically detect exceptional situations and problems and by notifying the medical staff of tasks that need to be performed, the computerized sedation guideline improves the execution of the guideline.

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.

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.

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

DTIC Science & Technology

2003-09-01

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

Catalog Descriptions Using VOTable Files

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

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

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...

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

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.

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

SU-F-P-36: Automation of Linear Accelerator Star Shot Measurement with Advanced XML Scripting and Electronic Portal Imaging Device

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

Nguyen, N; Knutson, N; Schmidt, M

Purpose: To verify a method used to automatically acquire jaw, MLC, collimator and couch star shots for a Varian TrueBeam linear accelerator utilizing Developer Mode and an Electronic Portal Imaging Device (EPID). Methods: An XML script was written to automate motion of the jaws, MLC, collimator and couch in TrueBeam Developer Mode (TBDM) to acquire star shot measurements. The XML script also dictates MV imaging parameters to facilitate automatic acquisition and recording of integrated EPID images. Since couch star shot measurements cannot be acquired using a combination of EPID and jaw/MLC collimation alone due to a fixed imager geometry, amore » method utilizing a 5mm wide steel ruler placed on the table and centered within a 15×15cm2 open field to produce a surrogate of the narrow field aperture was investigated. Four individual star shot measurements (X jaw, Y jaw, MLC and couch) were obtained using our proposed as well as traditional film-based method. Integrated EPID images and scanned measurement films were analyzed and compared. Results: Star shot (X jaw, Y jaw, MLC and couch) measurements were obtained in a single 5 minute delivery using the TBDM XML script method compared to 60 minutes for equivalent traditional film measurements. Analysis of the images and films demonstrated comparable isocentricity results, agreeing within 0.3mm of each other. Conclusion: The presented automatic approach of acquiring star shot measurements using TBDM and EPID has proven to be more efficient than the traditional film approach with equivalent results.« less

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).

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.

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: ...

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.

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.

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

PubMed

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

An introduction to the Semantic Web for health sciences librarians*

PubMed Central

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-01-01

Objectives: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. Methodology: The paper is structured into two main parts. “Semantic Web Technology” provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. “Semantic Web Applications and Research Projects in the Biomedical Field” is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Discussion and Conclusions: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. PMID:16636713

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

PubMed Central

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/ PMID:21713110

[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.

System on Mobile Devices Middleware: Thinking beyond Basic Phones and PDAs

NASA Astrophysics Data System (ADS)

Prasad, Sushil K.

Several classes of emerging applications, spanning domains such as medical informatics, homeland security, mobile commerce, and scientific applications, are collaborative, and a significant portion of these will harness the capabilities of both the stable and mobile infrastructures (the “mobile grid”). Currently, it is possible to develop a collaborative application running on a collection of heterogeneous, possibly mobile, devices, each potentially hosting data stores, using existing middleware technologies such as JXTA, BREW, Compact .NET and J2ME. However, they require too many ad-hoc techniques as well as cumbersome and time-consuming programming. Our System on Mobile Devices (SyD) middleware, on the other hand, has a modular architecture that makes such application development very systematic and streamlined. The architecture supports transactions over mobile data stores, with a range of remote group invocation options and embedded interdependencies among such data store objects. The architecture further provides a persistent uniform object view, group transaction with Quality of Service (QoS) specifications, and XML vocabulary for inter-device communication. I will present the basic SyD concepts, introduce the architecture and the design of the SyD middleware and its components. We will discuss the basic performance figures of SyD components and a few SyD applications on PDAs. SyD platform has led to developments in distributed web service coordination and workflow technologies, which we will briefly discuss. There is a vital need to develop methodologies and systems to empower common users, such as computational scientists, for rapid development of such applications. Our BondFlow system enables rapid configuration and execution of workflows over web services. The small footprint of the system enables them to reside on Java-enabled handheld devices.

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.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

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

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

Suggestions for Improvement of User Access to GOCE L2 Data

NASA Astrophysics Data System (ADS)

Tscherning, C. C.

2011-07-01

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

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.

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…

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.

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.

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

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

Implementation of workflow engine technology to deliver basic clinical decision support functionality

PubMed Central

2011-01-01

Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. Results We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. Conclusions We describe an implementation of a free workflow technology software suite (available at http://code.google.com/p/healthflow) and its application in the domain of clinical decision support. Our implementation seamlessly supports clinical logic testing on retrospective data and offers a user-friendly knowledge representation paradigm. With the presented software implementation, we demonstrate that workflow engine technology can provide a decision support platform which evaluates well against an established clinical decision support architecture evaluation framework. Due to cross-industry usage of workflow engine technology, we can expect significant future functionality enhancements that will further improve the technology's capacity to serve as a clinical decision support platform. PMID:21477364

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…

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

KLASS: Kennedy Launch Academy Simulation System

NASA Technical Reports Server (NTRS)

Garner, Lesley C.

2007-01-01

Software provides access to many sophisticated scientific instrumentation (Scanning Electron Microscope (SEM), a Light Microscope, a Scanning Probe Microscope (covering Scanning Tunneling, Atomic Force, and Magnetic Force microscopy), and an Energy Dispersive Spectrometer for the SEM). Flash animation videos explain how each of the instruments work. Videos on how they are used at NASA and the sample preparation. Measuring and labeling tools provided with each instrument. Hands on experience of controlling the virtual instrument to conduct investigations, much like the real scientists at NASA do. Very open architecture. Open source on SourceForge. Extensive use of XML Target audience is high school and entry-level college students. "Many beginning students never get closer to an electron microscope than the photos in their textbooks. But anyone can get a sense of what the instrument can do by downloading this simulator from NASA's Kennedy Space Center." Science Magazine, April 8th, 2005

Workflow in interventional radiology: uterine fibroid embolization (UFE)

NASA Astrophysics Data System (ADS)

Lindisch, David; Neumuth, Thomas; Burgert, Oliver; Spies, James; Cleary, Kevin

2008-03-01

Workflow analysis can be used to record the steps taken during clinical interventions with the goal of identifying bottlenecks and streamlining the procedure efficiency. In this study, we recorded the workflow for uterine fibroid embolization (UFE) procedures in the interventional radiology suite at Georgetown University Hospital in Washington, DC, USA. We employed a custom client/server software architecture developed by the Innovation Center for Computer Assisted Surgery (ICCAS) at the University of Leipzig, Germany. This software runs in a JAVA environment and enables an observer to record the actions taken by the physician and surgical team during these interventions. The data recorded is stored as an XML document, which can then be further processed. We recorded data from 30 patients and found a mean intervention time of 01:49:46 (+/- 16:04) minutes. The critical intervention step, the embolization, had a mean time of 00:15:42 (+/- 05:49) minutes, which was only 15% of the total intervention time.

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 ...

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)

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

NASA Astrophysics Data System (ADS)

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

2003-07-01

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

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.

Mercury- Distributed Metadata Management, Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Palanisamy, Giri; Wilson, Bruce E.; Devarakonda, Ranjeet; Green, James M.

2007-12-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source and ORNL- developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports various metadata standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115 (under development). Mercury provides a single portal to information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury supports various projects including: ORNL DAAC, NBII, DADDI, LBA, NARSTO, CDIAC, OCEAN, I3N, IAI, ESIP and ARM. The new Mercury system is based on a Service Oriented Architecture and supports various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. This system also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format.

PubMed

Ahmed, Zeeshan; Dandekar, Thomas

2015-01-01

Published scientific literature contains millions of figures, including information about the results obtained from different scientific experiments e.g. PCR-ELISA data, microarray analysis, gel electrophoresis, mass spectrometry data, DNA/RNA sequencing, diagnostic imaging (CT/MRI and ultrasound scans), and medicinal imaging like electroencephalography (EEG), magnetoencephalography (MEG), echocardiography  (ECG), positron-emission tomography (PET) images. The importance of biomedical figures has been widely recognized in scientific and medicine communities, as they play a vital role in providing major original data, experimental and computational results in concise form. One major challenge for implementing a system for scientific literature analysis is extracting and analyzing text and figures from published PDF files by physical and logical document analysis. Here we present a product line architecture based bioinformatics tool 'Mining Scientific Literature (MSL)', which supports the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied Optimal Character Recognition (OCR). Moreover, for further analysis and usage, it generates the system's output in different formats including text, PDF, XML and images files. Hence, MSL is an easy to install and use analysis tool to interpret published scientific literature in PDF format.

Implementation of Medical Information Exchange System Based on EHR Standard

PubMed Central

Han, Soon Hwa; Kim, Sang Guk; Jeong, Jun Yong; Lee, Bi Na; Choi, Myeong Seon; Kim, Il Kon; Park, Woo Sung; Ha, Kyooseob; Cho, Eunyoung; Kim, Yoon; Bae, Jae Bong

2010-01-01

Objectives To develop effective ways of sharing patients' medical information, we developed a new medical information exchange system (MIES) based on a registry server, which enabled us to exchange different types of data generated by various systems. Methods To assure that patient's medical information can be effectively exchanged under different system environments, we adopted the standardized data transfer methods and terminologies suggested by the Center for Interoperable Electronic Healthcare Record (CIEHR) of Korea in order to guarantee interoperability. Regarding information security, MIES followed the security guidelines suggested by the CIEHR of Korea. This study aimed to develop essential security systems for the implementation of online services, such as encryption of communication, server security, database security, protection against hacking, contents, and network security. Results The registry server managed information exchange as well as the registration information of the clinical document architecture (CDA) documents, and the CDA Transfer Server was used to locate and transmit the proper CDA document from the relevant repository. The CDA viewer showed the CDA documents via connection with the information systems of related hospitals. Conclusions This research chooses transfer items and defines document standards that follow CDA standards, such that exchange of CDA documents between different systems became possible through ebXML. The proposed MIES was designed as an independent central registry server model in order to guarantee the essential security of patients' medical information. PMID:21818447

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

Implementation of Medical Information Exchange System Based on EHR Standard.

PubMed

Han, Soon Hwa; Lee, Min Ho; Kim, Sang Guk; Jeong, Jun Yong; Lee, Bi Na; Choi, Myeong Seon; Kim, Il Kon; Park, Woo Sung; Ha, Kyooseob; Cho, Eunyoung; Kim, Yoon; Bae, Jae Bong

2010-12-01

To develop effective ways of sharing patients' medical information, we developed a new medical information exchange system (MIES) based on a registry server, which enabled us to exchange different types of data generated by various systems. To assure that patient's medical information can be effectively exchanged under different system environments, we adopted the standardized data transfer methods and terminologies suggested by the Center for Interoperable Electronic Healthcare Record (CIEHR) of Korea in order to guarantee interoperability. Regarding information security, MIES followed the security guidelines suggested by the CIEHR of Korea. This study aimed to develop essential security systems for the implementation of online services, such as encryption of communication, server security, database security, protection against hacking, contents, and network security. The registry server managed information exchange as well as the registration information of the clinical document architecture (CDA) documents, and the CDA Transfer Server was used to locate and transmit the proper CDA document from the relevant repository. The CDA viewer showed the CDA documents via connection with the information systems of related hospitals. This research chooses transfer items and defines document standards that follow CDA standards, such that exchange of CDA documents between different systems became possible through ebXML. The proposed MIES was designed as an independent central registry server model in order to guarantee the essential security of patients' medical information.

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.

A verification strategy for web services composition using enhanced stacked automata model.

PubMed

Nagamouttou, Danapaquiame; Egambaram, Ilavarasan; Krishnan, Muthumanickam; Narasingam, Poonkuzhali

2015-01-01

Currently, Service-Oriented Architecture (SOA) is becoming the most popular software architecture of contemporary enterprise applications, and one crucial technique of its implementation is web services. Individual service offered by some service providers may symbolize limited business functionality; however, by composing individual services from different service providers, a composite service describing the intact business process of an enterprise can be made. Many new standards have been defined to decipher web service composition problem namely Business Process Execution Language (BPEL). BPEL provides an initial work for forming an Extended Markup Language (XML) specification language for defining and implementing business practice workflows for web services. The problems with most realistic approaches to service composition are the verification of composed web services. It has to depend on formal verification method to ensure the correctness of composed services. A few research works has been carried out in the literature survey for verification of web services for deterministic system. Moreover the existing models did not address the verification properties like dead transition, deadlock, reachability and safetyness. In this paper, a new model to verify the composed web services using Enhanced Stacked Automata Model (ESAM) has been proposed. The correctness properties of the non-deterministic system have been evaluated based on the properties like dead transition, deadlock, safetyness, liveness and reachability. Initially web services are composed using Business Process Execution Language for Web Service (BPEL4WS) and it is converted into ESAM (combination of Muller Automata (MA) and Push Down Automata (PDA)) and it is transformed into Promela language, an input language for Simple ProMeLa Interpreter (SPIN) tool. The model is verified using SPIN tool and the results revealed better recital in terms of finding dead transition and deadlock in contrast to the existing models.

Building a High Performance Metadata Broker using Clojure, NoSQL and Message Queues

NASA Astrophysics Data System (ADS)

Truslove, I.; Reed, S.

2013-12-01

In practice, Earth and Space Science Informatics often relies on getting more done with less: fewer hardware resources, less IT staff, fewer lines of code. As a capacity-building exercise focused on rapid development of high-performance geoinformatics software, the National Snow and Ice Data Center (NSIDC) built a prototype metadata brokering system using a new JVM language, modern database engines and virtualized or cloud computing resources. The metadata brokering system was developed with the overarching goals of (i) demonstrating a technically viable product with as little development effort as possible, (ii) using very new yet very popular tools and technologies in order to get the most value from the least legacy-encumbered code bases, and (iii) being a high-performance system by using scalable subcomponents, and implementation patterns typically used in web architectures. We implemented the system using the Clojure programming language (an interactive, dynamic, Lisp-like JVM language), Redis (a fast in-memory key-value store) as both the data store for original XML metadata content and as the provider for the message queueing service, and ElasticSearch for its search and indexing capabilities to generate search results. On evaluating the results of the prototyping process, we believe that the technical choices did in fact allow us to do more for less, due to the expressive nature of the Clojure programming language and its easy interoperability with Java libraries, and the successful reuse or re-application of high performance products or designs. This presentation will describe the architecture of the metadata brokering system, cover the tools and techniques used, and describe lessons learned, conclusions, and potential next steps.

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.

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.

The PDS4 Information Model and its Role in Agile Science Data Curation

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Crichton, D.

2017-12-01

PDS4 is an information model-driven service architecture supporting the capture, management, distribution and integration of massive planetary science data captured in distributed data archives world-wide. The PDS4 Information Model (IM), the core element of the architecture, was developed using lessons learned from 20 years of archiving Planetary Science Data and best practices for information model development. The foundational principles were adopted from the Open Archival Information System (OAIS) Reference Model (ISO 14721), the Metadata Registry Specification (ISO/IEC 11179), and W3C XML (Extensible Markup Language) specifications. These provided respectively an object oriented model for archive information systems, a comprehensive schema for data dictionaries and hierarchical governance, and rules for rules for encoding documents electronically. The PDS4 Information model is unique in that it drives the PDS4 infrastructure by providing the representation of concepts and their relationships, constraints, rules, and operations; a sharable, stable, and organized set of information requirements; and machine parsable definitions that are suitable for configuring and generating code. This presentation will provide an over of the PDS4 Information Model and how it is being leveraged to develop and evolve the PDS4 infrastructure and enable agile curation of over 30 years of science data collected by the international Planetary Science community.

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…

Redefining the Data Pipeline Using GPUs

NASA Astrophysics Data System (ADS)

Warner, C.; Eikenberry, S. S.; Gonzalez, A. H.; Packham, C.

2013-10-01

There are two major challenges facing the next generation of data processing pipelines: 1) handling an ever increasing volume of data as array sizes continue to increase and 2) the desire to process data in near real-time to maximize observing efficiency by providing rapid feedback on data quality. Combining the power of modern graphics processing units (GPUs), relational database management systems (RDBMSs), and extensible markup language (XML) to re-imagine traditional data pipelines will allow us to meet these challenges. Modern GPUs contain hundreds of processing cores, each of which can process hundreds of threads concurrently. Technologies such as Nvidia's Compute Unified Device Architecture (CUDA) platform and the PyCUDA (http://mathema.tician.de/software/pycuda) module for Python allow us to write parallel algorithms and easily link GPU-optimized code into existing data pipeline frameworks. This approach has produced speed gains of over a factor of 100 compared to CPU implementations for individual algorithms and overall pipeline speed gains of a factor of 10-25 compared to traditionally built data pipelines for both imaging and spectroscopy (Warner et al., 2011). However, there are still many bottlenecks inherent in the design of traditional data pipelines. For instance, file input/output of intermediate steps is now a significant portion of the overall processing time. In addition, most traditional pipelines are not designed to be able to process data on-the-fly in real time. We present a model for a next-generation data pipeline that has the flexibility to process data in near real-time at the observatory as well as to automatically process huge archives of past data by using a simple XML configuration file. XML is ideal for describing both the dataset and the processes that will be applied to the data. Meta-data for the datasets would be stored using an RDBMS (such as mysql or PostgreSQL) which could be easily and rapidly queried and file I/O would be kept at a minimum. We believe this redefined data pipeline will be able to process data at the telescope, concurrent with continuing observations, thus maximizing precious observing time and optimizing the observational process in general. We also believe that using this design, it is possible to obtain a speed gain of a factor of 30-40 over traditional data pipelines when processing large archives of data.

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.

The use of geospatial web services for exchanging utilities data

NASA Astrophysics Data System (ADS)

Kuczyńska, Joanna

2013-04-01

Geographic information technologies and related geo-information systems currently play an important role in the management of public administration in Poland. One of these tasks is to maintain and update Geodetic Evidence of Public Utilities (GESUT), part of the National Geodetic and Cartographic Resource, which contains an important for many institutions information of technical infrastructure. It requires an active exchange of data between the Geodesy and Cartography Documentation Centers and institutions, which administrate transmission lines. The administrator of public utilities, is legally obliged to provide information about utilities to GESUT. The aim of the research work was to develop a universal data exchange methodology, which can be implemented on a variety of hardware and software platforms. This methodology use Unified Modeling Language (UML), eXtensible Markup Language (XML), and Geography Markup Language (GML). The proposed methodology is based on the two different strategies: Model Driven Architecture (MDA) and Service Oriented Architecture (SOA). Used solutions are consistent with the INSPIRE Directive and ISO 19100 series standards for geographic information. On the basis of analysis of the input data structures, conceptual models were built for both databases. Models were written in the universal modeling language: UML. Combined model that defines a common data structure was also built. This model was transformed into developed for the exchange of geographic information GML standard. The structure of the document describing the data that may be exchanged is defined in the .xsd file. Network services were selected and implemented in the system designed for data exchange based on open source tools. Methodology was implemented and tested. Data in the agreed data structure and metadata were set up on the server. Data access was provided by geospatial network services: data searching possibilities by Catalog Service for the Web (CSW), data collection by Web Feature Service (WFS). WFS provides also operation for modification data, for example to update them by utility administrator. The proposed solution significantly increases the efficiency of data exchange and facilitates maintenance the National Geodetic and Cartographic Resource.

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.

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

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

Converting from XML to HDF-EOS

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

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

A Leaner, Meaner Markup Language.

ERIC Educational Resources Information Center

Online & CD-ROM Review, 1997

1997-01-01

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

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.

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

Dcs Data Viewer, an Application that Accesses ATLAS DCS Historical Data

NASA Astrophysics Data System (ADS)

Tsarouchas, C.; Schlenker, S.; Dimitrov, G.; Jahn, G.

2014-06-01

The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. The Detector Control System (DCS) of ATLAS is responsible for the supervision of the detector equipment, the reading of operational parameters, the propagation of the alarms and the archiving of important operational data in a relational database (DB). DCS Data Viewer (DDV) is an application that provides access to the ATLAS DCS historical data through a web interface. Its design is structured using a client-server architecture. The pythonic server connects to the DB and fetches the data by using optimized SQL requests. It communicates with the outside world, by accepting HTTP requests and it can be used stand alone. The client is an AJAX (Asynchronous JavaScript and XML) interactive web application developed under the Google Web Toolkit (GWT) framework. Its web interface is user friendly, platform and browser independent. The selection of metadata is done via a column-tree view or with a powerful search engine. The final visualization of the data is done using java applets or java script applications as plugins. The default output is a value-over-time chart, but other types of outputs like tables, ascii or ROOT files are supported too. Excessive access or malicious use of the database is prevented by a dedicated protection mechanism, allowing the exposure of the tool to hundreds of inexperienced users. The current configuration of the client and of the outputs can be saved in an XML file. Protection against web security attacks is foreseen and authentication constrains have been taken into account, allowing the exposure of the tool to hundreds of users world wide. Due to its flexible interface and its generic and modular approach, DDV could be easily used for other experiment control systems.

Distributed framework for dyanmic telescope and instrument control

NASA Astrophysics Data System (ADS)

Ames, Troy J.; Case, Lynne

2003-02-01

Traditionally, instrument command and control systems have been developed specifically for a single instrument. Such solutions are frequently expensive and are inflexible to support the next instrument development effort. NASA Goddard Space Flight Center is developing an extensible framework, known as Instrument Remote Control (IRC) that applies to any kind of instrument that can be controlled by a computer. IRC 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 graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms. The IRC framework provides the ability to communicate to components anywhere on a network using the JXTA protocol for dynamic discovery of distributed components. JXTA (see http://www.jxta.org) is a generalized protocol that allows any devices connected by a network to communicate in a peer-to-peer manner. IRC uses JXTA to advertise a devices IML and discover devices of interest on the network. Devices can join or leave the network and thus join or leave the instrument control environment of IRC. Currently, several astronomical instruments are working with the IRC development team to develop custom components for IRC to control their instruments. These instruments include: High resolution Airborne Wideband Camera (HAWC), a first light instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA); Submillimeter And Far Infrared Experiment (SAFIRE), a Principal Investigator instrument for SOFIA; and Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE), a prototype of the SAFIRE instrument, used at the Caltech Submillimeter Observatory (CSO). Most recently, we have been working with the Submillimetre High

A Framework to Manage Information Models

NASA Astrophysics Data System (ADS)

Hughes, J. S.; King, T.; Crichton, D.; Walker, R.; Roberts, A.; Thieman, J.

2008-05-01

The Information Model is the foundation on which an Information System is built. It defines the entities to be processed, their attributes, and the relationships that add meaning. The development and subsequent management of the Information Model is the single most significant factor for the development of a successful information system. A framework of tools has been developed that supports the management of an information model with the rigor typically afforded to software development. This framework provides for evolutionary and collaborative development independent of system implementation choices. Once captured, the modeling information can be exported to common languages for the generation of documentation, application databases, and software code that supports both traditional and semantic web applications. This framework is being successfully used for several science information modeling projects including those for the Planetary Data System (PDS), the International Planetary Data Alliance (IPDA), the National Cancer Institute's Early Detection Research Network (EDRN), and several Consultative Committee for Space Data Systems (CCSDS) projects. The objective of the Space Physics Archive Search and Exchange (SPASE) program is to promote collaboration and coordination of archiving activity for the Space Plasma Physics community and ensure the compatibility of the architectures used for a global distributed system and the individual data centers. Over the past several years, the SPASE data model working group has made great progress in developing the SPASE Data Model and supporting artifacts including a data dictionary, XML Schema, and two ontologies. The authors have captured the SPASE Information Model in this framework. This allows the generation of documentation that presents the SPASE Information Model in object-oriented notation including UML class diagrams and class hierarchies. The modeling information can also be exported to semantic web languages such as OWL and RDF and written to XML Metadata Interchange (XMI) files for import into UML tools.

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.

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.…

Restful Implementation of Catalogue Service for Geospatial Data Provenance

NASA Astrophysics Data System (ADS)

Jiang, L. C.; Yue, P.; Lu, X. C.

2013-10-01

Provenance, also known as lineage, is important in understanding the derivation history of data products. Geospatial data provenance helps data consumers to evaluate the quality and reliability of geospatial data. In a service-oriented environment, where data are often consumed or produced by distributed services, provenance could be managed by following the same service-oriented paradigm. The Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) is used for the registration and query of geospatial data provenance by extending ebXML Registry Information Model (ebRIM). Recent advance of the REpresentational State Transfer (REST) paradigm has shown great promise for the easy integration of distributed resources. RESTful Web Service aims to provide a standard way for Web clients to communicate with servers based on REST principles. The existing approach for provenance catalogue service could be improved by adopting the RESTful design. This paper presents the design and implementation of a catalogue service for geospatial data provenance following RESTful architecture style. A middleware named REST Converter is added on the top of the legacy catalogue service to support a RESTful style interface. The REST Converter is composed of a resource request dispatcher and six resource handlers. A prototype service is developed to demonstrate the applicability of the approach.

A Generic Metadata Editor Supporting System Using Drupal CMS

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

PubMed

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

2003-01-01

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

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

PubMed Central

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

2003-01-01

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

Extending Phrase-Based Decoding with a Dependency-Based Reordering Model

DTIC Science & Technology

2009-11-01

strictly within the confines of phrase-based translation. The hope was to introduce an approach that could take advantage of monolingual syntactic...tuple represents one element of the XML markup, where element is the name of this element, attributes is a dictionary (mapping strings to strings...representing the range of possible compressions, in the form of a dictionary mapping the latter to the former. To represent multiple dependency

ICCE/ICCAI 2000 Full & Short Papers (Knowledge Construction and Navigation).

ERIC Educational Resources Information Center

2000

This document contains the following full and short papers on knowledge construction and navigation from ICCE/ICCAI 2000 (International Conference on Computers in Education/International Conference on Computer-Assisted Instruction): (1) "An XML-Based Tool for Building and Using Conceptual Maps in Education and Training Environments"…

Technological Minimalism: A Cost-Effective Alternative for Course Design and Development.

ERIC Educational Resources Information Center

Lorenzo, George

2001-01-01

Discusses the use of minimum levels of technology, or technological minimalism, for Web-based multimedia course content. Highlights include cost effectiveness; problems with video streaming, the use of XML for Web pages, and Flash and Java applets; listservs instead of proprietary software; and proper faculty training. (LRW)

Supporting Component-Based Courseware Development Using Virtual Apparatus Framework Script.

ERIC Educational Resources Information Center

Ip, Albert; Fritze, Paul

This paper reports on the latest development of the Virtual Apparatus (VA) framework, a contribution to efforts at the University of Melbourne (Australia) to mainstream content and pedagogical functions of curricula. The integration of the educational content and pedagogical functions of learning components using an XML compatible script,…

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

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

EPA Science Inventory

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

Development of the Plate Tectonics and Seismology markup languages with XML

NASA Astrophysics Data System (ADS)

Babaie, H.; Babaei, A.

2003-04-01

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

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

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

2015-10-01

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

A Semantic Analysis of XML Schema Matching for B2B Systems Integration

ERIC Educational Resources Information Center

Kim, Jaewook

2011-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

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

International Data | Geospatial Data Science | NREL

Science.gov Websites

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

An exponentiation method for XML element retrieval.

PubMed

Wichaiwong, Tanakorn

2014-01-01

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

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

PubMed

Ruminski, Jacek

2007-01-01

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

Bioinformatics data distribution and integration via Web Services and XML.

PubMed

Li, Xiao; Zhang, Yizheng

2003-11-01

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

QuakeML - An XML Schema for Seismology

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

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

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/).

Geospatial data sharing, online spatial analysis and processing of Indian Biodiversity data in Internet GIS domain - A case study for raster based online geo-processing

NASA Astrophysics Data System (ADS)

Karnatak, H.; Pandey, K.; Oberai, K.; Roy, A.; Joshi, D.; Singh, H.; Raju, P. L. N.; Krishna Murthy, Y. V. N.

2014-11-01

National Biodiversity Characterization at Landscape Level, a project jointly sponsored by Department of Biotechnology and Department of Space, was implemented to identify and map the potential biodiversity rich areas in India. This project has generated spatial information at three levels viz. Satellite based primary information (Vegetation Type map, spatial locations of road & village, Fire occurrence); geospatially derived or modelled information (Disturbance Index, Fragmentation, Biological Richness) and geospatially referenced field samples plots. The study provides information of high disturbance and high biological richness areas suggesting future management strategies and formulating action plans. The study has generated for the first time baseline database in India which will be a valuable input towards climate change study in the Indian Subcontinent. The spatial data generated during the study is organized as central data repository in Geo-RDBMS environment using PostgreSQL and POSTGIS. The raster and vector data is published as OGC WMS and WFS standard for development of web base geoinformation system using Service Oriented Architecture (SOA). The WMS and WFS based system allows geo-visualization, online query and map outputs generation based on user request and response. This is a typical mashup architecture based geo-information system which allows access to remote web services like ISRO Bhuvan, Openstreet map, Google map etc., with overlay on Biodiversity data for effective study on Bio-resources. The spatial queries and analysis with vector data is achieved through SQL queries on POSTGIS and WFS-T operations. But the most important challenge is to develop a system for online raster based geo-spatial analysis and processing based on user defined Area of Interest (AOI) for large raster data sets. The map data of this study contains approximately 20 GB of size for each data layer which are five in number. An attempt has been to develop system using python, PostGIS and PHP for raster data analysis over the web for Biodiversity conservation and prioritization. The developed system takes inputs from users as WKT, Openlayer based Polygon geometry and Shape file upload as AOI to perform raster based operation using Python and GDAL/OGR. The intermediate products are stored in temporary files and tables which generate XML outputs for web representation. The raster operations like clip-zip-ship, class wise area statistics, single to multi-layer operations, diagrammatic representation and other geo-statistical analysis are performed. This is indigenous geospatial data processing engine developed using Open system architecture for spatial analysis of Biodiversity data sets in Internet GIS environment. The performance of this applications in multi-user environment like Internet domain is another challenging task which is addressed by fine tuning the source code, server hardening, spatial indexing and running the process in load balance mode. The developed system is hosted in Internet domain (http://bis.iirs.gov.in) for user access.

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

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

PubMed

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

2005-08-01

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

XCEDE: An Extensible Schema For Biomedical Data

PubMed Central

Gadde, Syam; Aucoin, Nicole; Grethe, Jeffrey S.; Keator, David B.; Marcus, Daniel S.; Pieper, Steve

2013-01-01

The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing, describing and documenting the data generated by scientific studies. Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services. It provides a structured metadata hierarchy, storing information relevant to various aspects of an experiment (project, subject, protocol, etc.). Each hierarchy level also provides for the storage of data provenance information allowing for a traceable record of processing and/or changes to the underlying data. The schema is extensible to support the needs of various data modalities and to express types of data not originally envisioned by the developers. The latest version of the XCEDE schema and manual are available from http://www.xcede.org/ PMID:21479735

CliniProteus: A flexible clinical trials information management system

PubMed Central

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

2007-01-01

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

Gmz: a Gml Compression Model for Webgis

NASA Astrophysics Data System (ADS)

Khandelwal, A.; Rajan, K. S.

2017-09-01

Geography markup language (GML) is an XML specification for expressing geographical features. Defined by Open Geospatial Consortium (OGC), it is widely used for storage and transmission of maps over the Internet. XML schemas provide the convenience to define custom features profiles in GML for specific needs as seen in widely popular cityGML, simple features profile, coverage, etc. Simple features profile (SFP) is a simpler subset of GML profile with support for point, line and polygon geometries. SFP has been constructed to make sure it covers most commonly used GML geometries. Web Feature Service (WFS) serves query results in SFP by default. But it falls short of being an ideal choice due to its high verbosity and size-heavy nature, which provides immense scope for compression. GMZ is a lossless compression model developed to work for SFP compliant GML files. Our experiments indicate GMZ achieves reasonably good compression ratios and can be useful in WebGIS based applications.

Intelligent microchip networks: an agent-on-chip synthesis framework for the design of smart and robust sensor networks

NASA Astrophysics Data System (ADS)

Bosse, Stefan

2013-05-01

Sensorial materials consisting of high-density, miniaturized, and embedded sensor networks require new robust and reliable data processing and communication approaches. Structural health monitoring is one major field of application for sensorial materials. Each sensor node provides some kind of sensor, electronics, data processing, and communication with a strong focus on microchip-level implementation to meet the goals of miniaturization and low-power energy environments, a prerequisite for autonomous behaviour and operation. Reliability requires robustness of the entire system in the presence of node, link, data processing, and communication failures. Interaction between nodes is required to manage and distribute information. One common interaction model is the mobile agent. An agent approach provides stronger autonomy than a traditional object or remote-procedure-call based approach. Agents can decide for themselves, which actions are performed, and they are capable of flexible behaviour, reacting on the environment and other agents, providing some degree of robustness. Traditionally multi-agent systems are abstract programming models which are implemented in software and executed on program controlled computer architectures. This approach does not well scale to micro-chip level and requires full equipped computers and communication structures, and the hardware architecture does not consider and reflect the requirements for agent processing and interaction. We propose and demonstrate a novel design paradigm for reliable distributed data processing systems and a synthesis methodology and framework for multi-agent systems implementable entirely on microchip-level with resource and power constrained digital logic supporting Agent-On-Chip architectures (AoC). The agent behaviour and mobility is fully integrated on the micro-chip using pipelined communicating processes implemented with finite-state machines and register-transfer logic. The agent behaviour, interaction (communication), and mobility features are modelled and specified on a machine-independent abstract programming level using a state-based agent behaviour language (APL). With this APL a high-level agent compiler is able to synthesize a hardware model (RTL, VHDL), a software model (C, ML), or a simulation model (XML) suitable to simulate a multi-agent system using the SeSAm simulator framework. Agent communication is provided by a simple tuple-space database implemented on node level providing fault tolerant access of global data. A novel synthesis development kit (SynDK) based on a graph-structured database approach is introduced to support the rapid development of compilers and synthesis tools, used for example for the design and implementation of the APL compiler.

EO Domain Specific Knowledge Enabled Services (KES-B)

NASA Astrophysics Data System (ADS)

Varas, J.; Busto, J.; Torguet, R.

2004-09-01

This paper recovers and describes a number of major statements with respect to the vision, mission and technological approaches of the Technological Research Project (TRP) "EO Domain Specific Knowledge Enabled Services" (project acronym KES-B), which is currently under development at the European Space Research Institute (ESRIN) under contract "16397/02/I- SB". Resulting from the on-going R&D activities, the KES-B project aims are to demonstrate with a prototype system the feasibility of the application of innovative knowledge-based technologies to provide services for easy, scheduled and controlled exploitation of EO resources (e.g.: data, algorithms, procedures, storage, processors, ...), to automate the generation of products, and to support users in easily identifying and accessing the required information or products by using their own vocabulary, domain knowledge and preferences. The ultimate goals of KES-B are summarized in the provision of the two main types of KES services: 1st the Search service (also referred to as Product Exploitation or Information Retrieval; and 2nd the Production service (also referred to as Information Extraction), with the strategic advantage that they are enabled by Knowledge consolidated (formalized) within the system. The KES-B system technical solution approach is driven by a strong commitment for the adoption of industry (XML-based) language standards, aiming to have an interoperable, scalable and flexible operational prototype. In that sense, the Search KES services builds on the basis of the adoption of consolidated and/or emergent W3C semantic-web standards. Remarkably the languages/models Dublin Core (DC), Universal Resource Identifier (URI), Resource Description Framework (RDF) and Ontology Web Language (OWL), and COTS like Protege [1] and JENA [2] are being integrated in the system as building bricks for the construction of the KES based Search services. On the other hand, the Production KES services builds on top of workflow management standards and tools. In this side, the Business Process Execution Language (BPEL), the Web Services Definition Language (WSDL), and the Collaxa [3] COTS tool for workflow management are being integrated for the construction of the KES-B Production Services. The KES-B platform (web portal and web-server) architecture is build on the basis of the J2EE reference architecture. These languages represent the mean for the codification of the different types of knowledge that are to be formalized in the system. This representing the ontological architecture of the system. This shall enable in fact the interoperability with other KES-based systems committing as well to those standards. The motivation behind this vision is pointing towards the construction of the Semantic-web based GRID supply- chain infrastructure for EO-services, in line with the INSPIRE initiative suggestions.

Proper Plugin Protocols

DTIC Science & Technology

2011-12-28

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-15

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

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

ERIC Educational Resources Information Center

Walsh, Lucas

2007-01-01

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

WaterML: an XML Language for Communicating Water Observations Data

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

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.

A Novel Trust Service Provider for Internet Based Commerce Applications.

ERIC Educational Resources Information Center

Siyal, M. Y.; Barkat, B.

2002-01-01

Presents a framework for enhancing trust in Internet commerce. Shows how trust can be provided through a network of Trust Service Providers (TSp). Identifies a set of services that should be offered by a TSp. Presents a distributed object-oriented implementation of trust services using CORBA, JAVA and XML. (Author/AEF)

Perspectives for Electronic Books in the World Wide Web Age.

ERIC Educational Resources Information Center

Bry, Francois; Kraus, Michael

2002-01-01

Discusses the rapid growth of the World Wide Web and the lack of use of electronic books and suggests that specialized contents and device independence can make Web-based books compete with print. Topics include enhancing the hypertext model of XML; client-side adaptation, including browsers and navigation; and semantic modeling. (Author/LRW)

Symposium on Applications and the Internet (SAINT 2003) Proceedings (Orlando, Florida, January 27-31, 2003).

ERIC Educational Resources Information Center

Helal, Sumi, Ed.; Oie, Yuji, Ed.; Chang, Carl, Ed.; Murai, Jun, Ed.

This proceedings from the 2003 Symposium on Applications and the Internet (SAINT) contains papers from sessions on: (1) mobile Internet, including a target-driven cache replacement policy, context-awareness for service discovery, and XML transformation; (2) collaboration technology I, including human-network-based filtering, virtual collaboration…

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-08-01

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

Citing geospatial feature inventories with XML manifests

NASA Astrophysics Data System (ADS)

Bose, R.; McGarva, G.

2006-12-01

Today published scientific papers include a growing number of citations for online information sources that either complement or replace printed journals and books. We anticipate this same trend for cartographic citations used in the geosciences, following advances in web mapping and geographic feature-based services. Instead of using traditional libraries to resolve citations for print material, the geospatial citation life cycle will include requesting inventories of objects or geographic features from distributed geospatial data repositories. Using a case study from the UK Ordnance Survey MasterMap database, which is illustrative of geographic object-based products in general, we propose citing inventories of geographic objects using XML feature manifests. These manifests: (1) serve as a portable listing of sets of versioned features; (2) could be used as citations within the identification portion of an international geospatial metadata standard; (3) could be incorporated into geospatial data transfer formats such as GML; but (4) can be resolved only with comprehensive, curated repositories of current and historic data. This work has implications for any researcher who foresees the need to make or resolve references to online geospatial databases.

Systems of evidence-based healthcare and personalised health information: some international and national trends.

PubMed

Gordon, C; Gray, J A; Toth, B; Veloso, M

2000-01-01

In Europe, North America and elsewhere, growing interest has focussed on evidence-based healthcare systems, incorporating the deployment of practice guidelines, as a field of application for health telematics. The clinical benefit and technical feasibility of common European approaches to this task has recently been demonstrated. In Europe it is likely that, building on recent progress in electronic health record architecture (EHRA) standards, a sufficient state of maturity can be reached to justify initiation within CEN TC251 of a prestandards process on guideline content formats during the current 5th Framework of EC RT&D activity. There is now a similar impetus to agree standards for this field in North America. Thanks to fruitful EC-USA contacts during the 4th Framework programme, there is now a chance, given well-planned coordination, to establish a global consensus optimally suited to serve the world-wide delivery and application of evidence-based medicine. This review notes three factors which may accelerate progress to convergence: (1) revolutionary changes in the knowledge basis of professional/patient/public healthcare partnerships, involving the key role of the Web as a health knowledge resource for citizens, and a rapidly growing market for personalised health information and advice; (2) the emergence at national levels of digital warehouses of clinical guidelines and EBM knowledge resources, agencies which are capable of brokering common mark-up and interchange media definitions between knowledge providers, industry and healthcare organizations; (3) the closing gap in knowledge management technology, with the advent of XML and RDF, between approaches and services based respectively on text mark-up and knowledge-base paradigms. A current project in the UK National Health Service (the National electronic Library of Health) is cited as an example of a national initiative designed to harness these trends.

Data Sets and Data Services at the Northern California Earthquake Data Center

NASA Astrophysics Data System (ADS)

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

2014-12-01

The Northern California Earthquake Data Center (NCEDC) houses a unique and comprehensive data archive and provides real-time services for a variety of seismological and geophysical data sets that encompass northern and central California. We have over 80 terabytes of continuous and event-based time series data from broadband, short-period, strong motion, and strain sensors as well as continuous and campaign GPS data at both standard and high sample rates in both raw and RINEX format. The Northen California Seismic System (NCSS), operated by UC Berkeley and USGS Menlo Park, has recorded over 890,000 events from 1984 to the present, and the NCEDC provides catalog, parametric information, moment tensors and first motion mechanisms, and time series data for these events. We also host and provide event catalogs, parametric information, and event waveforms for DOE enhanced geothermal system monitoring in northern California and Nevada. The NCEDC provides a variety of ways for users to access these data. The most recent development are web services, which provide interactive, command-line, or program-based workflow access to data. Web services use well-established server and client protocols and RESTful software architecture that allow users to easily submit queries and receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, simple text, or MiniSEED depending on the service and selected output format. The NCEDC supports all FDSN-defined web services as well as a number of IRIS-defined and NCEDC-defined services. We also continue to support older email-based and browser-based access to data. NCEDC data and web services can be found at http://www.ncedc.org and http://service.ncedc.org.

Northern California Earthquake Data Center: Data Sets and Data Services

NASA Astrophysics Data System (ADS)

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

2015-12-01

The Northern California Earthquake Data Center (NCEDC) provides a permanent archive and real-time data distribution services for a unique and comprehensive data set of seismological and geophysical data sets encompassing northern and central California. We provide access to over 85 terabytes of continuous and event-based time series data from broadband, short-period, strong motion, and strain sensors as well as continuous and campaign GPS data at both standard and high sample rates. The Northen California Seismic System (NCSS), operated by UC Berkeley and USGS Menlo Park, has recorded over 900,000 events from 1984 to the present, and the NCEDC serves catalog, parametric information, moment tensors and first motion mechanisms, and time series data for these events. We also serve event catalogs, parametric information, and event waveforms for DOE enhanced geothermal system monitoring in northern California and Nevada. The NCEDC provides a several ways for users to access these data. The most recent development are web services, which provide interactive, command-line, or program-based workflow access to data. Web services use well-established server and client protocols and RESTful software architecture that allow users to easily submit queries and receive the requested data in real-time rather than through batch or email-based requests. Data are returned to the user in the appropriate format such as XML, RESP, simple text, or MiniSEED depending on the service and selected output format. The NCEDC supports all FDSN-defined web services as well as a number of IRIS-defined and NCEDC-defined services. We also continue to support older email-based and browser-based access to data. NCEDC data and web services can be found at http://www.ncedc.org and http://service.ncedc.org.

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format

PubMed Central

Ahmed, Zeeshan; Dandekar, Thomas

2018-01-01

Published scientific literature contains millions of figures, including information about the results obtained from different scientific experiments e.g. PCR-ELISA data, microarray analysis, gel electrophoresis, mass spectrometry data, DNA/RNA sequencing, diagnostic imaging (CT/MRI and ultrasound scans), and medicinal imaging like electroencephalography (EEG), magnetoencephalography (MEG), echocardiography  (ECG), positron-emission tomography (PET) images. The importance of biomedical figures has been widely recognized in scientific and medicine communities, as they play a vital role in providing major original data, experimental and computational results in concise form. One major challenge for implementing a system for scientific literature analysis is extracting and analyzing text and figures from published PDF files by physical and logical document analysis. Here we present a product line architecture based bioinformatics tool ‘Mining Scientific Literature (MSL)’, which supports the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied Optimal Character Recognition (OCR). Moreover, for further analysis and usage, it generates the system’s output in different formats including text, PDF, XML and images files. Hence, MSL is an easy to install and use analysis tool to interpret published scientific literature in PDF format. PMID:29721305

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

PubMed Central

Murphy, SN; Barnett, GO; Chueh, HC

2000-01-01

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

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

PubMed

Murphy; Barnett; Chueh

2000-01-01

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

Development of Web GIS for complex processing and visualization of climate geospatial datasets as an integral part of dedicated Virtual Research Environment

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

For comprehensive usage of large geospatial meteorological and climate datasets it is necessary to create a distributed software infrastructure based on the spatial data infrastructure (SDI) approach. Currently, it is generally accepted that the development of client applications as integrated elements of such infrastructure should be based on the usage of modern web and GIS technologies. The paper describes the Web GIS for complex processing and visualization of geospatial (mainly in NetCDF and PostGIS formats) datasets as an integral part of the dedicated Virtual Research Environment for comprehensive study of ongoing and possible future climate change, and analysis of their implications, providing full information and computing support for the study of economic, political and social consequences of global climate change at the global and regional levels. The Web GIS consists of two basic software parts: 1. Server-side part representing PHP applications of the SDI geoportal and realizing the functionality of interaction with computational core backend, WMS/WFS/WPS cartographical services, as well as implementing an open API for browser-based client software. Being the secondary one, this part provides a limited set of procedures accessible via standard HTTP interface. 2. Front-end part representing Web GIS client developed according to a "single page application" technology based on JavaScript libraries OpenLayers (http://openlayers.org/), ExtJS (https://www.sencha.com/products/extjs), GeoExt (http://geoext.org/). It implements application business logic and provides intuitive user interface similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. Boundless/OpenGeo architecture was used as a basis for Web-GIS client development. According to general INSPIRE requirements to data visualization Web GIS provides such standard functionality as data overview, image navigation, scrolling, scaling and graphical overlay, displaying map legends and corresponding metadata information. The specialized Web GIS client contains three basic tires: • Tier of NetCDF metadata in JSON format • Middleware tier of JavaScript objects implementing methods to work with: o NetCDF metadata o XML file of selected calculations configuration (XML task) o WMS/WFS/WPS cartographical services • Graphical user interface tier representing JavaScript objects realizing general application business logic Web-GIS developed provides computational processing services launching to support solving tasks in the area of environmental monitoring, as well as presenting calculation results in the form of WMS/WFS cartographical layers in raster (PNG, JPG, GeoTIFF), vector (KML, GML, Shape), and binary (NetCDF) formats. It has shown its effectiveness in the process of solving real climate change research problems and disseminating investigation results in cartographical formats. The work is supported by the Russian Science Foundation grant No 16-19-10257.

An Exponentiation Method for XML Element Retrieval

PubMed Central

2014-01-01

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

Maximizing data holdings and data documentation with a hierarchical system for sample-based geochemical data

NASA Astrophysics Data System (ADS)

Hsu, L.; Lehnert, K. A.; Walker, J. D.; Chan, C.; Ash, J.; Johansson, A. K.; Rivera, T. A.

2011-12-01

Sample-based measurements in geochemistry are highly diverse, due to the large variety of sample types, measured properties, and idiosyncratic analytical procedures. In order to ensure the utility of sample-based data for re-use in research or education they must be associated with a high quality and quantity of descriptive, discipline-specific metadata. Without an adequate level of documentation, it is not possible to reproduce scientific results or have confidence in using the data for new research inquiries. The required detail in data documentation makes it challenging to aggregate large sets of data from different investigators and disciplines. One solution to this challenge is to build data systems with several tiers of intricacy, where the less detailed tiers are geared toward discovery and interoperability, and the more detailed tiers have higher value for data analysis. The Geoinformatics for Geochemistry (GfG) group, which is part of the Integrated Earth Data Applications facility (http://www.iedadata.org), has taken this approach to provide services for the discovery, access, and analysis of sample-based geochemical data for a diverse user community, ranging from the highly informed geochemist to non-domain scientists and undergraduate students. GfG builds and maintains three tiers in the sample based data systems, from a simple data catalog (Geochemical Resource Library), to a substantially richer data model for the EarthChem Portal (EarthChem XML), and finally to detailed discipline-specific data models for petrologic (PetDB), sedimentary (SedDB), hydrothermal spring (VentDB), and geochronological (GeoChron) samples. The data catalog, the lowest level in the hierarchy, contains the sample data values plus metadata only about the dataset itself (Dublin Core metadata such as dataset title and author), and therefore can accommodate the widest diversity of data holdings. The second level includes measured data values from the sample, basic information about the analytical method, and metadata about the samples such as geospatial information and sample type. The third and highest level includes detailed data quality documentation and more specific information about the scientific context of the sample. The three tiers are linked to allow users to quickly navigate to their desired level of metadata detail. Links are based on the use of unique identifiers: (a) DOI at the granularity of datasets, and (b) the International Geo Sample Number IGSN at the granularity of samples. Current developments in the GfG sample-based systems include new registry architecture for the IGSN to advance international implementation, growth and modification of EarthChemXML to include geochemical data for new sample types such as soils and liquids, and the construction of a hydrothermal vent data system. This flexible, tiered, model provides a solution for offering varying levels of detail in order to aggregate a large quantity of data and serve the largest user group of both disciplinary novices and experts.

Report of Official foreign Travel to Spain April 17-29, 1999. (in English;)

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

Mason, j.d.

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 in preference to 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)more » 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), which DOE has selected as the basis of its electronic management of documents. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML, and its use is likely to increase in the future. 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 Microsoft, Adobe, and Netscape, is promoting XML ("eXtensible Markup Language"), a class of SGML applications, for the future of the WWW and the basis for EC. W3C has announced its intention of discontinuing future development of HTML and replacing it with XHTML, an application of XML. 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 April 1999 trip, I convened the spring 1999 meeting of SC34 in Granada, Spain. I also attended a major conference on the use of SGML and XML. SC34 maintains and continues to enhance several standards. In addition to SGML, which is the basis of HTML and XML, SC34 also works on the Document Style Semantics and Specification Language (DSSSL), which is the basis for W3C's XSL ("eXtensible Style Language," to be used with XML) and the Hypermedia/Time-based Document Structuring Language (HyTime), which is a major influence on W3C's XLink ("XML Linking Language"). SC34 is also involved in work with ISO's TC184, Industrial Data, on the linking of STEP (the standard for the interchange of product model data) with SGML. 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 Y-12 Plant. My project team in Information Technology Services 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). Supporting standards development allows DOE and the Y-12 plant both input into the process and the opportunity 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 Model for Open Access Journal Publication

PubMed Central

Blesius, Carl R.; Williams, Michael A.; Holzbach, Ana; Huntley, Arthur C.; Chueh, Henry

2005-01-01

We describe an electronic journal publication infrastructure that allows a flexible publication workflow, academic exchange around different forms of user submissions, and the exchange of articles between publishers and archives using a common XML based standard. This web-based application is implemented on a freely available open source software stack. This publication demonstrates the Dermatology Online Journal's use of the platform for non-biased independent open access publication. PMID:16779183

Taming Log Files from Game/Simulation-Based Assessments: Data Models and Data Analysis Tools. Research Report. ETS RR-16-10

ERIC Educational Resources Information Center

Hao, Jiangang; Smith, Lawrence; Mislevy, Robert; von Davier, Alina; Bauer, Malcolm

2016-01-01

Extracting information efficiently from game/simulation-based assessment (G/SBA) logs requires two things: a well-structured log file and a set of analysis methods. In this report, we propose a generic data model specified as an extensible markup language (XML) schema for the log files of G/SBAs. We also propose a set of analysis methods for…

A new archival infrastructure for highly-structured astronomical data

NASA Astrophysics Data System (ADS)

Dovgan, Erik; Knapic, Cristina; Sponza, Massimo; Smareglia, Riccardo

2018-03-01

With the advent of the 2020 Radio Astronomy Telescopes era, the amount and format of the radioastronomical data is becoming a massive and performance-critical challenge. Such an evolution of data models and data formats require new data archiving techniques that allow massive and fast storage of data that are at the same time also efficiently processed. A useful expertise for efficient archiviation has been obtained through data archiving of Medicina and Noto Radio Telescopes. The presented archival infrastructure named the Radio Archive stores and handles various formats, such as FITS, MBFITS, and VLBI's XML, which includes description and ancillary files. The modeling and architecture of the archive fulfill all the requirements of both data persistence and easy data discovery and exploitation. The presented archive already complies with the Virtual Observatory directives, therefore future service implementations will also be VO compliant. This article presents the Radio Archive services and tools, from the data acquisition to the end-user data utilization.

Workflow in interventional radiology: nerve blocks and facet blocks

NASA Astrophysics Data System (ADS)

Siddoway, Donald; Ingeholm, Mary Lou; Burgert, Oliver; Neumuth, Thomas; Watson, Vance; Cleary, Kevin

2006-03-01

Workflow analysis has the potential to dramatically improve the efficiency and clinical outcomes of medical procedures. In this study, we recorded the workflow for nerve block and facet block procedures in the interventional radiology suite at Georgetown University Hospital in Washington, DC, USA. We employed a custom client/server software architecture developed by the Innovation Center for Computer Assisted Surgery (ICCAS) at the University of Leipzig, Germany. This software runs in an internet browser, and allows the user to record the actions taken by the physician during a procedure. The data recorded during the procedure is stored as an XML document, which can then be further processed. We have successfully gathered data on a number if cases using a tablet PC, and these preliminary results show the feasibility of using this software in an interventional radiology setting. We are currently accruing additional cases and when more data has been collected we will analyze the workflow of these procedures to look for inefficiencies and potential improvements.

ArdenML: The Arden Syntax Markup Language (or Arden Syntax: It's Not Just Text Any More!)

PubMed Central

Sailors, R. Matthew

2001-01-01

It is no longer necessary to think of Arden Syntax as simply a text-based knowledge base format. The development of ArdenML (Arden Syntax Markup Language), an XML-based markup language allows structured access to most of the maintenance and library categories without the need to write or buy a compiler may lead to the development of simple commercial and freeware tools for processing Arden Syntax Medical Logic Modules (MLMs)

Automated Test Methods for XML Metadata

DTIC Science & Technology

2017-12-28

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

Aircraft

DTIC Science & Technology

2003-01-01

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

Schema for Spacecraft-Command Dictionary

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

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.