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

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...

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.

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.

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.

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.

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.

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

Development of geotechnical data schema in transportation : final report.

DOT National Transportation Integrated Search

2012-12-01

The objective of "Development of Geotechnical Data Schema in Transportation" is to develop an : international standard interchange format for geotechnical data. This standard will include a data : dictionary and XML schema which are GML compliant. Th...

An XML Data Model for Inverted Image Indexing

NASA Astrophysics Data System (ADS)

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

2003-01-01

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

A 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/).

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.

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

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.

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

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.

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

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.

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

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

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

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.

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.

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.

Use of standard vocabulary services in validation of water resources data

NASA Astrophysics Data System (ADS)

Yu, Jonathan; Cox, Simon; Ratcliffe, David

2010-05-01

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

The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

PubMed Central

Kang, Hyunseok P.; Borromeo, Charles D.; Berman, Jules J.; Becich, Michael J.

2010-01-01

Background: Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject-Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts. PMID:20805954

An adaptable XML based approach for scientific data management and integration

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

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

PubMed

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

2008-02-20

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

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

PubMed

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

2008-06-01

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

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.

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.

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.

The Graphical Representation of the Digital Astronaut Physiology Backbone

NASA Technical Reports Server (NTRS)

Briers, Demarcus

2010-01-01

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

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.

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 Service Environment for Enhanced Knowledge and Research (SEEKR) Framework

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

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

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

NASA Astrophysics Data System (ADS)

Staley, Tim D.

2014-11-01

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

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

PubMed

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

2006-01-01

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

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.

Learn about the Environmental Information Exchange Network

EPA Pesticide Factsheets

States, territories, and tribes can partner with EPA to exchange standardized data to improve its quality, increase its availability, and integrate it better across different sources using connecting nodes, xml schema, and a data exchange template.

CytometryML: a markup language for analytical cytology

NASA Astrophysics Data System (ADS)

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

2003-06-01

Cytometry Markup Language, CytometryML, is a proposed new analytical cytology data standard. CytometryML is a set of XML schemas for encoding both flow cytometry and digital microscopy text based data types. CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. These schemas provide representations for the keywords in FCS 3.0 and will soon include DICOM microscopic image data. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. A preliminary version of a list mode binary data type, which does not presently exist in DICOM, has been designed. This binary type is required to enhance the storage and transmission of flow cytometry and digital microscopy data. Index files based on Waveform indices will be used to rapidly locate the cells present in individual subsets. DICOM has the advantage of employing standard file types, TIF and JPEG, for Digital Microscopy. Using an XML schema based representation means that standard commercial software packages such as Excel and MathCad can be used to analyze, display, and store analytical cytometry data. Furthermore, by providing one standard for both DICOM data and analytical cytology data, it eliminates the need to create and maintain special purpose interfaces for analytical cytology data thereby integrating the data into the larger DICOM and other clinical communities. A draft version of CytometryML is available at www.newportinstruments.com.

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

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

EPA Pesticide Factsheets

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

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

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.

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.

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

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.

Enabling knowledge discovery: taxonomy development for NASA

NASA Technical Reports Server (NTRS)

Dutra, J.; Busch, J.

2003-01-01

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

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

PubMed

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

2013-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Sharing Epigraphic Information as Linked Data

NASA Astrophysics Data System (ADS)

Álvarez, Fernando-Luis; García-Barriocanal, Elena; Gómez-Pantoja, Joaquín-L.

The diffusion of epigraphic data has evolved in the last years from printed catalogues to indexed digital databases shared through the Web. Recently, the open EpiDoc specifications have resulted in an XML-based schema for the interchange of ancient texts that uses XSLT to render typographic representations. However, these schemas and representation systems are still not providing a way to encode computational semantics and semantic relations between pieces of epigraphic data. This paper sketches an approach to bring these semantics into an EpiDoc based schema using the Ontology Web Language (OWL) and following the principles and methods of information sharing known as "linked data". The paper describes the general principles of the OWL mapping of the EpiDoc schema and how epigraphic data can be shared in RDF format via dereferenceable URIs that can be used to build advanced search, visualization and analysis systems.

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.

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

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

PubMed

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

2012-07-01

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

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

PubMed Central

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

2012-01-01

Abstract In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML. PMID:22357728

Minimum information required for a DMET experiment reporting.

PubMed

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

2016-09-01

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

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

NASA Astrophysics Data System (ADS)

Benedict, K. K.; Scott, S.

2013-12-01

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

A JEE RESTful service to access Conditions Data in ATLAS

NASA Astrophysics Data System (ADS)

Formica, Andrea; Gallas, E. J.

2015-12-01

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

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.

Utilization of Forward Error Correction (FEC) Techniques With Extensible Markup Language (XML) Schema-Based Binary Compression (XSBC) Technology

DTIC Science & Technology

2004-12-01

NY 7. Erik Chaum NUWC Newport, RI 8. David Bellino NPRI Newport, RI 9. Dick Nadolink NUWC Newport, RI 10. VADM Roger Bacon (Ret...Science Advisor Pearl Harbor, HI 16. LT Andrew Hurvitz, USN FNMOC Monterey, CA 17. ENS Darin Keeter, USN FNMOC Monterey, CA 18. CAPT David

A Learning Design Ontology Based on the IMS Specification

ERIC Educational Resources Information Center

Amorim, Ricardo R.; Lama, Manuel; Sanchez, Eduardo; Riera, Adolfo; Vila, Xose A.

2006-01-01

In this paper, we present an ontology to represent the semantics of the IMS Learning Design (IMS LD) specification, a meta-language used to describe the main elements of the learning design process. The motivation of this work relies on the expressiveness limitations found on the current XML-Schema implementation of the IMS LD conceptual model. To…

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.

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.

An RDF version of the VO Registry Version 1.00

NASA Astrophysics Data System (ADS)

Gray, Norman; Gray, Norman

2007-09-01

We describe the initial implementation of an RDF version of the IVOA Resource Registry, serving the registry data via a SPARQL query endpoint, including the creation of the ontology analogues of an important subset of the relevant XML Schemas, and the mechanics of the conversion process. The result is an experimental service, and this is an interim document.

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

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-05

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

DialysisNet: Application for Integrating and Management Data Sources of Hemodialysis Information by Continuity of Care Record.

PubMed

Ku, Ho Suk; Kim, Sungho; Kim, HyeHyeon; Chung, Hee-Joon; Park, Yu Rang; Kim, Ju Han

2014-04-01

Health Avatar Beans was for the management of chronic kidney disease and end-stage renal disease (ESRD). This article is about the DialysisNet system in Health Avatar Beans for the seamless management of ESRD based on the personal health record. For hemodialysis data modeling, we identified common data elements for hemodialysis information (CDEHI). We used ASTM continuity of care record (CCR) and ISO/IEC 11179 for the compliance method with a standard model for the CDEHI. According to the contents of the ASTM CCR, we mapped the CDHEI to the contents and created the metadata from that. It was transformed and parsed into the database and verified according to the ASTM CCR/XML schema definition (XSD). DialysisNet was created as an iPad application. The contents of the CDEHI were categorized for effective management. For the evaluation of information transfer, we used CarePlatform, which was developed for data access. The metadata of CDEHI in DialysisNet was exchanged by the CarePlatform with semantic interoperability. The CDEHI was separated into a content list for individual patient data, a contents list for hemodialysis center data, consultation and transfer form, and clinical decision support data. After matching to the CCR, the CDEHI was transformed to metadata, and it was transformed to XML and proven according to the ASTM CCR/XSD. DialysisNet has specific consideration of visualization, graphics, images, statistics, and database. We created the DialysisNet application, which can integrate and manage data sources for hemodialysis information based on CCR standards.

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.

Cytometry metadata in XML

NASA Astrophysics Data System (ADS)

Leif, Robert C.; Leif, Stephanie H.

2016-04-01

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

CytometryML: a data standard which has been designed to interface with other standards

NASA Astrophysics Data System (ADS)

Leif, Robert C.

2007-02-01

Because of the differences in the requirements, needs, and past histories including existing standards of the creating organizations, a single encompassing cytology-pathology standard will not, in the near future, replace the multiple existing or under development standards. Except for DICOM and FCS, these standardization efforts are all based on XML. CytometryML is a collection of XML schemas, which are based on the Digital Imaging and Communications in Medicine (DICOM) and Flow Cytometry Standard (FCS) datatypes. The CytometryML schemas contain attributes that link them to the DICOM standard and FCS. Interoperability with DICOM has been facilitated by, wherever reasonable, limiting the difference between CytometryML and the previous standards to syntax. In order to permit the Resource Description Framework, RDF, to reference the CytometryML datatypes, id attributes have been added to many CytometryML elements. The Laboratory Digital Imaging Project (LDIP) Data Exchange Specification and the Flowcyt standards development effort employ RDF syntax. Documentation from DICOM has been reused in CytometryML. The unity of analytical cytology was demonstrated by deriving a microscope type and a flow cytometer type from a generic cytometry instrument type. The feasibility of incorporating the Flowcyt gating schemas into CytometryML has been demonstrated. CytometryML is being extended to include many of the new DICOM Working Group 26 datatypes, which describe patients, specimens, and analytes. In situations where multiple standards are being created, interoperability can be facilitated by employing datatypes based on a common set of semantics and building in links to standards that employ different syntax.

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

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.

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

NASA Astrophysics Data System (ADS)

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

2010-10-01

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

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.

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.

Producing a Data Dictionary from an Extensible Markup Language (XML) Schemain the Global Force Management Data Initiative

DTIC Science & Technology

2017-02-01

entity relationship (diagram) EwID Enterprise-wide Identifier FMID Force Management Identifier GFM Global Force Management HTML Hypertext Markup Language... Management Data Initiative by Frederick S Brundick Approved for public release; distribution is unlimited. NOTICES Disclaimers The findings in this report...Schema in the Global Force Management Data Initiative by Frederick S Brundick Computing and Information Sciences Directorate, ARL Approved for public

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…

An Approach to Information Management for AIR7000 with Metadata and Ontologies

DTIC Science & Technology

2009-10-01

metadata. We then propose an approach based on Semantic Technologies including the Resource Description Framework (RDF) and Upper Ontologies, for the...mandating specific metadata schemas can result in interoperability problems. For example, many standards within the ADO mandate the use of XML for metadata...such problems, we propose an archi- tecture in which different metadata schemes can inter operate. By using RDF (Resource Description Framework ) as a

Java-Library for the Access, Storage and Editing of Calibration Metadata of Optical Sensors

NASA Astrophysics Data System (ADS)

Firlej, M.; Kresse, W.

2016-06-01

The standardization of the calibration of optical sensors in photogrammetry and remote sensing has been discussed for more than a decade. Projects of the German DGPF and the European EuroSDR led to the abstract International Technical Specification ISO/TS 19159-1:2014 "Calibration and validation of remote sensing imagery sensors and data - Part 1: Optical sensors". This article presents the first software interface for a read- and write-access to all metadata elements standardized in the ISO/TS 19159-1. This interface is based on an xml-schema that was automatically derived by ShapeChange from the UML-model of the Specification. The software interface serves two cases. First, the more than 300 standardized metadata elements are stored individually according to the xml-schema. Secondly, the camera manufacturers are using many administrative data that are not a part of the ISO/TS 19159-1. The new software interface provides a mechanism for input, storage, editing, and output of both types of data. Finally, an output channel towards a usual calibration protocol is provided. The interface is written in Java. The article also addresses observations made when analysing the ISO/TS 19159-1 and compiles a list of proposals for maturing the document, i.e. for an updated version of the Specification.

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

NASA Astrophysics Data System (ADS)

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

2000-10-01

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

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

On-line interactive virtual experiments on nanoscience

NASA Astrophysics Data System (ADS)

Kadar, Manuella; Ileana, Ioan; Hutanu, Constantin

2009-01-01

This paper is an overview on the next generation web which allows students to experience virtual experiments on nano science, physics devices, processes and processing equipment. Virtual reality is used to support a real university lab in which a student can experiment real lab sessions. The web material is presented in an intuitive and highly visual 3D form that is accessible to a diverse group of students. Such type of laboratory provides opportunities for professional and practical education for a wide range of users. The expensive equipment and apparatuses that build the experimental stage in a particular standard laboratory is used to create virtual educational research laboratories. Students learn how to prepare the apparatuses and facilities for the experiment. The online experiments metadata schema is the format for describing online experiments, much like the schema behind a library catalogue used to describe the books in a library. As an online experiment is a special kind of learning object, one specifies its schema as an extension to an established metadata schema for learning objects. The content of the courses, metainformation as well as readings and user data are saved on the server in a database as XML objects.

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

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2010-08-25

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Space-Time Coordinate Metadata for the Virtual Observatory Version 1.33

NASA Astrophysics Data System (ADS)

Rots, A. H.; Rots, A. H.

2007-10-01

This document provides a complete design description of the Space-Time Coordinate (STC) metadata for the Virtual Observatory. It explains the various components, highlights some implementation considerations, presents a complete set of UML diagrams, and discusses the relation between STC and certain other parts of the Data Model. Two serializations are discussed: XML Schema (STC-X) and String (STC-S); the former is an integral part of this Recommendation.

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

PubMed Central

Lyal, Christopher H. C.

2016-01-01

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

Development Of International Data Standards For The COSMOS/PEER-LL Virtual Data Center

NASA Astrophysics Data System (ADS)

Swift, J. N.

2005-12-01

The COSMOS -PEER Lifelines Project 2L02 completed a Pilot Geotechnical Virtual Data Center (GVDC) system capable of both archiving geotechnical data and of disseminating data from multiple linked geotechnical databases. The Pilot GVDC system links geotechnical databases of four organizations: the California Geological Survey, Caltrans, PG&E, and the U. S. Geological Survey The System was presented and reviewed in the COSMOS-PEER Lifelines workshop on June 21 - 23, 2004, which was co-sponsored by the Federal Highway Administration (FHWA) and included participation by the United Kingdom Highways Agency (UKHA) , the Association of Geotechnical and Geoenvironmental Specialists in the United Kingdom (AGS), the United States Army Corp of Engineers (USACOE), Caltrans, United States Geological Survey (USGS), California Geological Survey (CGS), a number of state Departments of Transportation (DOTs), county building code officials, and representatives of academic institutions and private sector geotechnical companies. As of February 2005 COSMOS-PEER Lifelines Project 2L03 is currently funded to accomplish the following tasks: 1) expand the Pilot GVDC Geotechnical Data Dictionary and XML Schema to include data definitions and structures to describe in-situ measurements such as shear wave velocity profiles, and additional laboratory geotechnical test types; 2) participate in an international cooperative working group developing a single geotechnical data exchange standard that has broad international acceptance; and 3) upgrade the GVDC system to support corresponding exchange standard data dictionary and schema improvements. The new geophysical data structures being developed will include PS-logs, downhole geophysical logs, cross-hole velocity data, and velocity profiles derived using surface waves. A COSMOS-PEER Lifelines Geophysical Data Dictionary Working Committee constituted of experts in the development of data dictionary standards and experts in the specific data to be captured are presently working on this task. The international geotechnical data dictionary and schema development is a highly collaborative effort funded by a pooled fund study coordinated by state DOTs and FHWA. The technical development of the standards called DIGGS (Data Interchange for Geotechnical and Geoenvironmental Specialists) is lead by a team consisting of representatives from the University of Florida, Department of Civil Engineering (UF), AGS, Construction Industry Research and Information Association (CIRIA), UKHA, Ohio DOT, and COSMOS. The first draft of DIGGS is currently in preparation. A Geotechnical Management System Group (GMS group), composed of representatives from 13 State DOTs, FHWA, US EPA, USACOE, USGS and UKHA, oversees and approves the development of the standards. The ultimate goal of both COSMOS-PEER Lifelines Project 2L03 and the international GMS working group is to produce open and flexible, GML-compliant XML schema-based data structures and data dictionaries for review and approval by DOTs, other public agencies, and the international engineering and geoenvironmental community at large, leading to adoption of internationally accepted geotechnical and geophysical data transfer standards. Establishment of these standards is intended to significantly facilitate the accessibility and exchange of geotechnical information world wide.

Design and implementation of CUAHSI WaterML and WaterOneFlow Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Zaslavsky, I.; Whitenack, T.; Maidment, D.

2007-12-01

WaterOneFlow is a term for a group of web services created by and for the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) community. CUAHSI web services facilitate the retrieval of hydrologic observations information from online data sources using the SOAP protocol. CUAHSI Water Markup Language (below referred to as WaterML) is an XML schema defining the format of messages returned by the WaterOneFlow web services. \

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

NASA Astrophysics Data System (ADS)

Zaytsev, A.

2010-04-01

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

Efficient Workflows for Curation of Heterogeneous Data Supporting Modeling of U-Nb Alloy Aging

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

Ward, Logan Timothy; Hackenberg, Robert Errol

These are slides from a presentation summarizing a graduate research associate's summer project. The following topics are covered in these slides: data challenges in materials, aging in U-Nb Alloys, Building an Aging Model, Different Phase Trans. in U-Nb, the Challenge, Storing Materials Data, Example Data Source, Organizing Data: What is a Schema?, What does a "XML Schema" look like?, Our Data Schema: Nice and Simple, Storing Data: Materials Data Curation System (MDCS), Problem with MDCS: Slow Data Entry, Getting Literature into MDCS, Staging Data in Excel Document, Final Result: MDCS Records, Analyzing Image Data, Process for Making TTT Diagram, Bottleneckmore » Number 1: Image Analysis, Fitting a TTP Boundary, Fitting a TTP Curve: Comparable Results, How Does it Compare to Our Data?, Image Analysis Workflow, Curating Hardness Records, Hardness Data: Two Key Decisions, Before Peak Age? - Automation, Interactive Viz, Which Transformation?, Microstructure-Informed Model, Tracking the Entire Process, General Problem with Property Models, Pinyon: Toolkit for Managing Model Creation, Tracking Individual Decisions, Jupyter: Docs and Code in One File, Hardness Analysis Workflow, Workflow for Aging Models, and conclusions.« less

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

PubMed

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

2013-07-23

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

Design and implementation of the mobility assessment tool: software description

PubMed Central

2013-01-01

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

Characterizing Thematized Derivative Schema by the Underlying Emergent Structures

ERIC Educational Resources Information Center

Garcia, Mercedes; Llinares, Salvador; Sanchez-Matamoros, Gloria

2011-01-01

This paper reports on different underlying structures of the derivative schema of three undergraduate students that were considered to be at the trans level of development of the derivative schema (action-process-object-schema). The derivative schema is characterized in terms of the students' ability to explicitly transfer the relationship between…

TAPRegExt: a VOResource Schema Extension for Describing TAP Services Version 1.0

NASA Astrophysics Data System (ADS)

Demleitner, Markus; Dowler, Patrick; Plante, Ray; Rixon, Guy; Taylor, Mark; Demleitner, Markus

2012-08-01

This document describes an XML encoding standard for metadata about services implementing the table access protocol TAP [TAP], referred to as TAPRegExt. Instance documents are part of the service's registry record or can be obtained from the service itself. They deliver information to both humans and software on the languages, output formats, and upload methods supported by the service, as well as data models implemented by the exposed tables, optional language features, and certain limits enforced by the service.

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.

How we see others: the psychobiology of schemas and transference.

PubMed

Stein, Dan J

2009-01-01

Social cognition involves automatic and stimulus-driven processes; these may be important in mediating stereotypes in the community and schemas and transference in the clinic setting. Significant differences in self-related processing and other-related processing may also lead to important biases in our view of the other. The psychobiology of social cognition is gradually being delineated, and may be useful in understanding these phenomena, and in responding appropriately. In the clinic, schemas can be rigorously assessed, and schema-focused psychotherapy may be useful in a number of indications.

A Proposal for a Thesaurus for Web Services in Solar Radiation

NASA Technical Reports Server (NTRS)

Gschwind, Benoit; Menard, Lionel; Ranchin, Thierry; Wald, Lucien; Stackhouse, Paul W., Jr.

2007-01-01

Metadata are necessary to discover, describe and exchange any type of information, resource and service at a large scale. A significant amount of effort has been made in the field of geography and environment to establish standards. Efforts still remain to address more specific domains such as renewable energies. This communication focuses on solar energy and more specifically on aspects in solar radiation that relate to geography and meteorology. A thesaurus in solar radiation is proposed for the keys elements in solar radiation namely time, space and radiation types. The importance of time-series in solar radiation is outlined and attributes of the key elements are discussed. An XML schema for encoding metadata is proposed. The exploitation of such a schema in web services is discussed. This proposal is a first attempt at establishing a thesaurus for describing data and applications in solar radiation.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

PubMed

Kalas, Matús; Puntervoll, Pål; Joseph, Alexandre; Bartaseviciūte, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

2010-09-15

The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.

Towards the Development of a Unified Distributed Date System for L1 Spacecraft

NASA Technical Reports Server (NTRS)

Lazarus, Alan J.; Kasper, Justin C.

2005-01-01

The purpose of this grant, 'Towards the Development of a Unified Distributed Data System for L1 Spacecraft', is to take the initial steps towards the development of a data distribution mechanism for making in-situ measurements more easily accessible to the scientific community. Our obligations as subcontractors to this grant are to add our Faraday Cup plasma data to this initial study and to contribute to the design of a general data distribution system. The year 1 objectives of the overall project as stated in the GSFC proposal are: 1) Both the rsync and Perl based data exchange tools will be fully developed and tested in our mixed, Unix, VMS, Windows and Mac OS X data service environment. Based on the performance comparisons, one will be selected and fully deployed. Continuous data exchange between all L1 solar wind monitors initiated. 2) Data version metadata will be agreed upon, fully documented, and deployed on our data sites. 3) The first version of the data description rules, encoded in a XML Schema, will be finalized. 4) Preliminary set of library routines will be collected, documentation standards and formats agreed on, and desirable routines that have not been implemented identified and assigned. 5) ViSBARD test site implemented to independently validate data mirroring procedures. The specific MIT tasks over the duration of this project are the following: a) implement mirroring service for WIND plasma data b) participate in XML Schema development c) contribute toward routine library.

Qcorp: an annotated classification corpus of Chinese health questions.

PubMed

Guo, Haihong; Na, Xu; Li, Jiao

2018-03-22

Health question-answering (QA) systems have become a typical application scenario of Artificial Intelligent (AI). An annotated question corpus is prerequisite for training machines to understand health information needs of users. Thus, we aimed to develop an annotated classification corpus of Chinese health questions (Qcorp) and make it openly accessible. We developed a two-layered classification schema and corresponding annotation rules on basis of our previous work. Using the schema, we annotated 5000 questions that were randomly selected from 5 Chinese health websites within 6 broad sections. 8 annotators participated in the annotation task, and the inter-annotator agreement was evaluated to ensure the corpus quality. Furthermore, the distribution and relationship of the annotated tags were measured by descriptive statistics and social network map. The questions were annotated using 7101 tags that covers 29 topic categories in the two-layered schema. In our released corpus, the distribution of questions on the top-layered categories was treatment of 64.22%, diagnosis of 37.14%, epidemiology of 14.96%, healthy lifestyle of 10.38%, and health provider choice of 4.54% respectively. Both the annotated health questions and annotation schema were openly accessible on the Qcorp website. Users can download the annotated Chinese questions in CSV, XML, and HTML format. We developed a Chinese health question corpus including 5000 manually annotated questions. It is openly accessible and would contribute to the intelligent health QA system development.

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

Standards-based curation of a decade-old digital repository dataset of molecular information.

PubMed

Harvey, Matthew J; Mason, Nicholas J; McLean, Andrew; Murray-Rust, Peter; Rzepa, Henry S; Stewart, James J P

2015-01-01

The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.

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.

Model-Driven Engineering of Machine Executable Code

NASA Astrophysics Data System (ADS)

Eichberg, Michael; Monperrus, Martin; Kloppenburg, Sven; Mezini, Mira

Implementing static analyses of machine-level executable code is labor intensive and complex. We show how to leverage model-driven engineering to facilitate the design and implementation of programs doing static analyses. Further, we report on important lessons learned on the benefits and drawbacks while using the following technologies: using the Scala programming language as target of code generation, using XML-Schema to express a metamodel, and using XSLT to implement (a) transformations and (b) a lint like tool. Finally, we report on the use of Prolog for writing model transformations.

The version control service for the ATLAS data acquisition configuration files

NASA Astrophysics Data System (ADS)

Soloviev, Igor

2012-12-01

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

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

PubMed Central

Sun, Shanghua; Hassan, Taher; Kalra, Dipak

2013-01-01

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

A Low-Storage-Consumption XML Labeling Method for Efficient Structural Information Extraction

NASA Astrophysics Data System (ADS)

Liang, Wenxin; Takahashi, Akihiro; Yokota, Haruo

Recently, labeling methods to extract and reconstruct the structural information of XML data, which are important for many applications such as XPath query and keyword search, are becoming more attractive. To achieve efficient structural information extraction, in this paper we propose C-DO-VLEI code, a novel update-friendly bit-vector encoding scheme, based on register-length bit operations combining with the properties of Dewey Order numbers, which cannot be implemented in other relevant existing schemes such as ORDPATH. Meanwhile, the proposed method also achieves lower storage consumption because it does not require either prefix schema or any reserved codes for node insertion. We performed experiments to evaluate and compare the performance and storage consumption of the proposed method with those of the ORDPATH method. Experimental results show that the execution times for extracting depth information and parent node labels using the C-DO-VLEI code are about 25% and 15% less, respectively, and the average label size using the C-DO-VLEI code is about 24% smaller, comparing with ORDPATH.

NCPP's Use of Standard Metadata to Promote Open and Transparent Climate Modeling

NASA Astrophysics Data System (ADS)

Treshansky, A.; Barsugli, J. J.; Guentchev, G.; Rood, R. B.; DeLuca, C.

2012-12-01

The National Climate Predictions and Projections (NCPP) Platform is developing comprehensive regional and local information about the evolving climate to inform decision making and adaptation planning. This includes both creating and providing tools to create metadata about the models and processes used to create its derived data products. NCPP is using the Common Information Model (CIM), an ontology developed by a broad set of international partners in climate research, as its metadata language. This use of a standard ensures interoperability within the climate community as well as permitting access to the ecosystem of tools and services emerging alongside the CIM. The CIM itself is divided into a general-purpose (UML & XML) schema which structures metadata documents, and a project or community-specific (XML) Controlled Vocabulary (CV) which constraints the content of metadata documents. NCPP has already modified the CIM Schema to accommodate downscaling models, simulations, and experiments. NCPP is currently developing a CV for use by the downscaling community. Incorporating downscaling into the CIM will lead to several benefits: easy access to the existing CIM Documents describing CMIP5 models and simulations that are being downscaled, access to software tools that have been developed in order to search, manipulate, and visualize CIM metadata, and coordination with national and international efforts such as ES-DOC that are working to make climate model descriptions and datasets interoperable. Providing detailed metadata descriptions which include the full provenance of derived data products will contribute to making that data (and, the models and processes which generated that data) more open and transparent to the user community.

BioXSD: the common data-exchange format for everyday bioinformatics web services

PubMed Central

Kalaš, Matúš; Puntervoll, Pæl; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge

2010-01-01

Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types. Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web. Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community. Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org PMID:20823319

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.

Leverage and Delegation in Developing an Information Model for Geology

NASA Astrophysics Data System (ADS)

Cox, S. J.

2007-12-01

GeoSciML is an information model and XML encoding developed by a group of primarily geologic survey organizations under the auspices of the IUGS CGI. The scope of the core model broadly corresponds with information traditionally portrayed on a geologic map, viz. interpreted geology, some observations, the map legend and accompanying memoir. The development of GeoSciML has followed the methodology specified for an Application Schema defined by OGC and ISO 19100 series standards. This requires agreement within a community concerning their domain model, its formal representation using UML, documentation as a Feature Type Catalogue, with an XML Schema implementation generated from the model by applying a rule-based transformation. The framework and technology supports a modular governance process. Standard datatypes and GI components (geometry, the feature and coverage metamodels, metadata) are imported from the ISO framework. The observation and sampling model (including boreholes) is imported from OGC. The scale used for most scalar literal values (terms, codes, measures) allows for localization where necessary. Wildcards and abstract base- classes provide explicit extensibility points. Link attributes appear in a regular way in the encodings, allowing reference to external resources using URIs. The encoding is compatible with generic GI data-service interfaces (WFS, WMS, SOS). For maximum interoperability within a community, the interfaces may be specialised through domain-specified constraints (e.g. feature-types, scale and vocabulary bindings, query-models). Formalization using UML and XML allows use of standard validation and processing tools. Use of upper-level elements defined for generic GI application reduces the development effort and governance resonsibility, while maximising cross-domain interoperability. On the other hand, enabling specialization to be delegated in a controlled manner is essential to adoption across a range of subdisciplines and jurisdictions. The GeoSciML design team is responsible only for the part of the model that is unique to geology but for which general agreement can be reached within the domain. This paper is presented on behalf of the Interoperability Working Group of the IUGS Commission for Geoscience Information (CGI) - follow web-link for details of the membership.

Metadata Sets for e-Government Resources: The Extended e-Government Metadata Schema (eGMS+)

NASA Astrophysics Data System (ADS)

Charalabidis, Yannis; Lampathaki, Fenareti; Askounis, Dimitris

In the dawn of the Semantic Web era, metadata appear as a key enabler that assists management of the e-Government resources related to the provision of personalized, efficient and proactive services oriented towards the real citizens’ needs. As different authorities typically use different terms to describe their resources and publish them in various e-Government Registries that may enhance the access to and delivery of governmental knowledge, but also need to communicate seamlessly at a national and pan-European level, the need for a unified e-Government metadata standard emerges. This paper presents the creation of an ontology-based extended metadata set for e-Government Resources that embraces services, documents, XML Schemas, code lists, public bodies and information systems. Such a metadata set formalizes the exchange of information between portals and registries and assists the service transformation and simplification efforts, while it can be further taken into consideration when applying Web 2.0 techniques in e-Government.

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.

The Therapeutic Alliance in Schema-Focused Therapy and Transference-Focused Psychotherapy for Borderline Personality Disorder

ERIC Educational Resources Information Center

Spinhoven, Philip; Giesen-Bloo, Josephine; van Dyck, Richard; Kooiman, Kees; Arntz, Arnoud

2007-01-01

This study investigated the quality and development of the therapeutic alliance as a mediator of change in schema-focused therapy (SFT) and transference-focused psychotherapy (TFP) for borderline personality disorder. Seventy-eight patients were randomly allocated to 3 years of biweekly SFT or TFP. Scores of both therapists and patients for the…

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.

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.

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

NASA Astrophysics Data System (ADS)

Lake, Ron

2005-11-01

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

Schema Theories as a Base for the Structural Representation of the Knowledge State.

ERIC Educational Resources Information Center

Dochy, F. J. R. C.; Bouwens, M. R. J.

From the view of schema-transfer theory, the use of schemata with their several functions gives an explanation for the facilitative effect of prior knowledge on learning processes. This report gives a theoretical exploration of the concept of schemata, underlying schema theories, and functions of schemata to indicate the importance of schema…

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.

Multi-facetted Metadata - Describing datasets with different metadata schemas at the same time

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Klump, Jens; Bertelmann, Roland

2013-04-01

Inspired by the wish to re-use research data a lot of work is done to bring data systems of the earth sciences together. Discovery metadata is disseminated to data portals to allow building of customized indexes of catalogued dataset items. Data that were once acquired in the context of a scientific project are open for reappraisal and can now be used by scientists that were not part of the original research team. To make data re-use easier, measurement methods and measurement parameters must be documented in an application metadata schema and described in a written publication. Linking datasets to publications - as DataCite [1] does - requires again a specific metadata schema and every new use context of the measured data may require yet another metadata schema sharing only a subset of information with the meta information already present. To cope with the problem of metadata schema diversity in our common data repository at GFZ Potsdam we established a solution to store file-based research data and describe these with an arbitrary number of metadata schemas. Core component of the data repository is an eSciDoc infrastructure that provides versioned container objects, called eSciDoc [2] "items". The eSciDoc content model allows assigning files to "items" and adding any number of metadata records to these "items". The eSciDoc items can be submitted, revised, and finally published, which makes the data and metadata available through the internet worldwide. GFZ Potsdam uses eSciDoc to support its scientific publishing workflow, including mechanisms for data review in peer review processes by providing temporary web links for external reviewers that do not have credentials to access the data. Based on the eSciDoc API, panMetaDocs [3] provides a web portal for data management in research projects. PanMetaDocs, which is based on panMetaWorks [4], is a PHP based web application that allows to describe data with any XML-based schema. It uses the eSciDoc infrastructures REST-interface to store versioned dataset files and metadata in a XML-format. The software is able to administrate more than one eSciDoc metadata record per item and thus allows the description of a dataset according to its context. The metadata fields can be filled with static or dynamic content to reduce the number of fields that require manual entries to a minimum and, at the same time, make use of contextual information available in a project setting. Access rights can be adjusted to set visibility of datasets to the required degree of openness. Metadata from separate instances of panMetaDocs can be syndicated to portals through RSS and OAI-PMH interfaces. The application architecture presented here allows storing file-based datasets and describe these datasets with any number of metadata schemas, depending on the intended use case. Data and metadata are stored in the same entity (eSciDoc items) and are managed by a software tool through the eSciDoc REST interface - in this case the application is panMetaDocs. Other software may re-use the produced items and modify the appropriate metadata records by accessing the web API of the eSciDoc data infrastructure. For presentation of the datasets in a web browser we are not bound to panMetaDocs. This is done by stylesheet transformation of the eSciDoc-item. [1] http://www.datacite.org [2] http://www.escidoc.org , eSciDoc, FIZ Karlruhe, Germany [3] http://panmetadocs.sf.net , panMetaDocs, GFZ Potsdam, Germany [4] http://metaworks.pangaea.de , panMetaWorks, Dr. R. Huber, MARUM, Univ. Bremen, Germany

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.

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

PubMed

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

2007-01-01

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

Arranging ISO 13606 archetypes into a knowledge base.

PubMed

Kopanitsa, Georgy

2014-01-01

To enable the efficient reuse of standard based medical data we propose to develop a higher level information model that will complement the archetype model of ISO 13606. This model will make use of the relationships that are specified in UML to connect medical archetypes into a knowledge base within a repository. UML connectors were analyzed for their ability to be applied in the implementation of a higher level model that will establish relationships between archetypes. An information model was developed using XML Schema notation. The model allows linking different archetypes of one repository into a knowledge base. Presently it supports several relationships and will be advanced in future.

Creating preservation metadata from XML-metadata profiles

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

PubMed

Eminaga, O; Semjonow, A; Oezguer, E; Herden, J; Akbarov, I; Tok, A; Engelmann, U; Wille, S

2014-01-01

The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

Schematic memory components converge within angular gyrus during retrieval

PubMed Central

Wagner, Isabella C; van Buuren, Mariët; Kroes, Marijn CW; Gutteling, Tjerk P; van der Linden, Marieke; Morris, Richard G; Fernández, Guillén

2015-01-01

Mental schemas form associative knowledge structures that can promote the encoding and consolidation of new and related information. Schemas are facilitated by a distributed system that stores components separately, presumably in the form of inter-connected neocortical representations. During retrieval, these components need to be recombined into one representation, but where exactly such recombination takes place is unclear. Thus, we asked where different schema components are neuronally represented and converge during retrieval. Subjects acquired and retrieved two well-controlled, rule-based schema structures during fMRI on consecutive days. Schema retrieval was associated with midline, medial-temporal, and parietal processing. We identified the multi-voxel representations of different schema components, which converged within the angular gyrus during retrieval. Critically, convergence only happened after 24-hour-consolidation and during a transfer test where schema material was applied to novel but related trials. Therefore, the angular gyrus appears to recombine consolidated schema components into one memory representation. DOI: http://dx.doi.org/10.7554/eLife.09668.001 PMID:26575291

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

Arranging ISO 13606 archetypes into a knowledge base using UML connectors.

PubMed

Kopanitsa, Georgy

2014-01-01

To enable the efficient reuse of standard based medical data we propose to develop a higher-level information model that will complement the archetype model of ISO 13606. This model will make use of the relationships that are specified in UML to connect medical archetypes into a knowledge base within a repository. UML connectors were analysed for their ability to be applied in the implementation of a higher-level model that will establish relationships between archetypes. An information model was developed using XML Schema notation. The model allows linking different archetypes of one repository into a knowledge base. Presently it supports several relationships and will be advanced in future.

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.

Telescope networking and user support via Remote Telescope Markup Language

NASA Astrophysics Data System (ADS)

Hessman, Frederic V.; Pennypacker, Carlton R.; Romero-Colmenero, Encarni; Tuparev, Georg

2004-09-01

Remote Telescope Markup Language (RTML) is an XML-based interface/document format designed to facilitate the exchange of astronomical observing requests and results between investigators and observatories as well as within networks of observatories. While originally created to support simple imaging telescope requests (Versions 1.0-2.1), RTML Version 3.0 now supports a wide range of applications, from request preparation, exposure calculation, spectroscopy, and observation reports to remote telescope scheduling, target-of-opportunity observations and telescope network administration. The elegance of RTML is that all of this is made possible using a public XML Schema which provides a general-purpose, easily parsed, and syntax-checked medium for the exchange of astronomical and user information while not restricting or otherwise constraining the use of the information at either end. Thus, RTML can be used to connect heterogeneous systems and their users without requiring major changes in existing local resources and procedures. Projects as very different as a number of advanced amateur observatories, the global Hands-On Universe project, the MONET network (robotic imaging), the STELLA consortium (robotic spectroscopy), and the 11-m Southern African Large Telescope are now using or intending to use RTML in various forms and for various purposes.

Mass spectrometer output file format mzML.

PubMed

Deutsch, Eric W

2010-01-01

Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products.

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

NASA Astrophysics Data System (ADS)

Stepien, Bernard; Felty, Amy; Matwin, Stan

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

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.

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.

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

A data management infrastructure for bridge monitoring

NASA Astrophysics Data System (ADS)

Jeong, Seongwoon; Byun, Jaewook; Kim, Daeyoung; Sohn, Hoon; Bae, In Hwan; Law, Kincho H.

2015-04-01

This paper discusses a data management infrastructure framework for bridge monitoring applications. As sensor technologies mature and become economically affordable, their deployment for bridge monitoring will continue to grow. Data management becomes a critical issue not only for storing the sensor data but also for integrating with the bridge model to support other functions, such as management, maintenance and inspection. The focus of this study is on the effective data management of bridge information and sensor data, which is crucial to structural health monitoring and life cycle management of bridge structures. We review the state-of-the-art of bridge information modeling and sensor data management, and propose a data management framework for bridge monitoring based on NoSQL database technologies that have been shown useful in handling high volume, time-series data and to flexibly deal with unstructured data schema. Specifically, Apache Cassandra and Mongo DB are deployed for the prototype implementation of the framework. This paper describes the database design for an XML-based Bridge Information Modeling (BrIM) schema, and the representation of sensor data using Sensor Model Language (SensorML). The proposed prototype data management framework is validated using data collected from the Yeongjong Bridge in Incheon, Korea.

Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.

PubMed

Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Incremental checking of Master Data Management model based on contextual graphs

NASA Astrophysics Data System (ADS)

Lamolle, Myriam; Menet, Ludovic; Le Duc, Chan

2015-10-01

The validation of models is a crucial step in distributed heterogeneous systems. In this paper, an incremental validation method is proposed in the scope of a Model Driven Engineering (MDE) approach, which is used to develop a Master Data Management (MDM) field represented by XML Schema models. The MDE approach presented in this paper is based on the definition of an abstraction layer using UML class diagrams. The validation method aims to minimise the model errors and to optimisethe process of model checking. Therefore, the notion of validation contexts is introduced allowing the verification of data model views. Description logics specify constraints that the models have to check. An experimentation of the approach is presented through an application developed in ArgoUML IDE.

Prior schemata transfer as an account for assessing the intuitive use of new technology.

PubMed

Fischer, Sandrine; Itoh, Makoto; Inagaki, Toshiyuki

2015-01-01

New devices are considered intuitive when they allow users to transfer prior knowledge. Drawing upon fundamental psychology experiments that distinguish prior knowledge transfer from new schema induction, a procedure was specified for assessing intuitive use. This procedure was tested with 31 participants who, prior to using an on-board computer prototype, studied its screenshots in reading vs. schema induction conditions. Distinct patterns of transfer or induction resulted for features of the prototype whose functions were familiar or unfamiliar, respectively. Though moderated by participants' cognitive style, these findings demonstrated a means for quantitatively assessing transfer of prior knowledge as the operation that underlies intuitive use. Implications for interface evaluation and design, as well as potential improvements to the procedure, are discussed. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Physical Samples and Persistent Identifiers: The Implementation of the International Geo Sample Number (IGSN) Registration Service in CSIRO, Australia

NASA Astrophysics Data System (ADS)

Devaraju, Anusuriya; Klump, Jens; Tey, Victor; Fraser, Ryan

2016-04-01

Physical samples such as minerals, soil, rocks, water, air and plants are important observational units for understanding the complexity of our environment and its resources. They are usually collected and curated by different entities, e.g., individual researchers, laboratories, state agencies, or museums. Persistent identifiers may facilitate access to physical samples that are scattered across various repositories. They are essential to locate samples unambiguously and to share their associated metadata and data systematically across the Web. The International Geo Sample Number (IGSN) is a persistent, globally unique label for identifying physical samples. The IGSNs of physical samples are registered by end-users (e.g., individual researchers, data centers and projects) through allocating agents. Allocating agents are the institutions acting on behalf of the implementing organization (IGSN e.V.). The Commonwealth Scientific and Industrial Research Organisation CSIRO) is one of the allocating agents in Australia. To implement IGSN in our organisation, we developed a RESTful service and a metadata model. The web service enables a client to register sub-namespaces and multiple samples, and retrieve samples' metadata programmatically. The metadata model provides a framework in which different types of samples may be represented. It is generic and extensible, therefore it may be applied in the context of multi-disciplinary projects. The metadata model has been implemented as an XML schema and a PostgreSQL database. The schema is used to handle sample registrations requests and to disseminate their metadata, whereas the relational database is used to preserve the metadata records. The metadata schema leverages existing controlled vocabularies to minimize the scope for error and incorporates some simplifications to reduce complexity of the schema implementation. The solutions developed have been applied and tested in the context of two sample repositories in CSIRO, the Capricorn Distal Footprints project and the Rock Store.

Modeling and validating HL7 FHIR profiles using semantic web Shape Expressions (ShEx).

PubMed

Solbrig, Harold R; Prud'hommeaux, Eric; Grieve, Grahame; McKenzie, Lloyd; Mandel, Joshua C; Sharma, Deepak K; Jiang, Guoqian

2017-03-01

HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation. Create a FHIR to ShEx model transformation and assess its ability to describe and validate FHIR RDF data. We created the methods and tools that generate the ShEx schemas modeling the FHIR to RDF specification being developed by HL7 ITS/W3C RDF Task Force, and evaluated the applicability of ShEx in the description and validation of FHIR to RDF transformations. The ShEx models contributed significantly to workgroup consensus. Algorithmic transformations from the FHIR model to ShEx schemas and FHIR example data to RDF transformations were incorporated into the FHIR build process. ShEx schemas representing 109 FHIR resources were used to validate 511 FHIR RDF data examples from the Standards for Trial Use (STU 3) Ballot version. We were able to uncover unresolved issues in the FHIR to RDF specification and detect 10 types of errors and root causes in the actual implementation. The FHIR ShEx representations have been included in the official FHIR web pages for the STU 3 Ballot version since September 2016. ShEx can be used to define and validate the syntax of a FHIR resource, which is complementary to the use of RDF Schema (RDFS) and Web Ontology Language (OWL) for semantic validation. ShEx proved useful for describing a standard model of FHIR RDF data. The combination of a formal model and a succinct format enabled comprehensive review and automated validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Come to think of it: Contributions of reasoning abilities and training schedule to skill acquisition in a virtual throwing task.

PubMed

Frömer, Romy; Stürmer, Birgit; Sommer, Werner

2016-10-01

According to Schmidt's schema theory skill acquisition is based on schema formation where multiple learning incidents with varying task features are abstracted to a unifying pattern, the schema. Practice can be scheduled block-wise, with low contextual interference (CI) or randomly, with high CI. The greater effort during high CI training usually results in reduced training success but enhanced retention and transfer performance. In contrast to well-established CI effects for simple tasks, findings for complex tasks are heterogeneous, supposedly due to the detrimental accumulation of task demands. We assumed that in complex tasks, cognitive reasoning abilities might impose a limit upon schema formation and hence the effectiveness of CI. In a virtual overarm-throwing experiment participants practiced target positions at center, left, or right and were retested for retention - at the center position - and transfer with a larger target distance. Although there was no main effect of CI on performance, either in training, retention or transfer, under high CI, training performance was better for participants with higher reasoning ability, as measured with the Raven matrices. This advantage persisted across retention and transfer. Under low CI, reasoning was positively related to performance improvement only in the last third of training. We argue, that variability of practice is a necessary prerequisite for beneficial effects of reasoning abilities. Based on previous findings, we discuss feedback evaluation as a possible locus of the relationship between reasoning and performance in motor skill acquisition. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2010-04-01

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

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

PubMed

Masseroli, Marco; Marchente, Mario

2008-07-01

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

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

PubMed Central

Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa; Aranda, Bruno; Quinn, Antony F; Vinod, Nisha; Bader, Gary D; Xenarios, Ioannis; Wojcik, Jérôme; Sherman, David; Tyers, Mike; Salama, John J; Moore, Susan; Ceol, Arnaud; Chatr-aryamontri, Andrew; Oesterheld, Matthias; Stümpflen, Volker; Salwinski, Lukasz; Nerothin, Jason; Cerami, Ethan; Cusick, Michael E; Vidal, Marc; Gilson, Michael; Armstrong, John; Woollard, Peter; Hogue, Christopher; Eisenberg, David; Cesareni, Gianni; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel. PMID:17925023

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.

Telemetry Attributes Transfer Standard (TMATS) Handbook

DTIC Science & Technology

2015-07-01

Example ......................... 6-1 Appendix A. Extensible Markup Language TMATS Differences ...................................... A-1 Appendix B...return-to-zero - level TG Telemetry Group TM telemetry TMATS Telemetry Attributes Transfer Standard XML eXtensible Markup Language Telemetry... Markup Language) format. The initial version of a standard 1 Range Commanders Council. Telemetry

FastSim: A Fast Simulation for the SuperB Detector

NASA Astrophysics Data System (ADS)

Andreassen, R.; Arnaud, N.; Brown, D. N.; Burmistrov, L.; Carlson, J.; Cheng, C.-h.; Di Simone, A.; Gaponenko, I.; Manoni, E.; Perez, A.; Rama, M.; Roberts, D.; Rotondo, M.; Simi, G.; Sokoloff, M.; Suzuki, A.; Walsh, J.

2011-12-01

We have developed a parameterized (fast) simulation for detector optimization and physics reach studies of the proposed SuperB Flavor Factory in Italy. Detector components are modeled as thin sections of planes, cylinders, disks or cones. Particle-material interactions are modeled using simplified cross-sections and formulas. Active detectors are modeled using parameterized response functions. Geometry and response parameters are configured using xml files with a custom-designed schema. Reconstruction algorithms adapted from BaBar are used to build tracks and clusters. Multiple sources of background signals can be merged with primary signals. Pattern recognition errors are modeled statistically by randomly misassigning nearby tracking hits. Standard BaBar analysis tuples are used as an event output. Hadronic B meson pair events can be simulated at roughly 10Hz.

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology

PubMed Central

Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines. PMID:29023519

GeoSciML and EarthResourceML Update, 2012

NASA Astrophysics Data System (ADS)

Richard, S. M.; Commissionthe Management; Application Inte, I.

2012-12-01

CGI Interoperability Working Group activities during 2012 include deployment of services using the GeoSciML-Portrayal schema, addition of new vocabularies to support properties added in version 3.0, improvements to server software for deploying services, introduction of EarthResourceML v.2 for mineral resources, and collaboration with the IUSS on a markup language for soils information. GeoSciML and EarthResourceML have been used as the basis for the INSPIRE Geology and Mineral Resources specifications respectively. GeoSciML-Portrayal is an OGC GML simple-feature application schema for presentation of geologic map unit, contact, and shear displacement structure (fault and ductile shear zone) descriptions in web map services. Use of standard vocabularies for geologic age and lithology enables map services using shared legends to achieve visual harmonization of maps provided by different services. New vocabularies have been added to the collection of CGI vocabularies provided to support interoperable GeoSciML services, and can be accessed through http://resource.geosciml.org. Concept URIs can be dereferenced to obtain SKOS rdf or html representations using the SISSVoc vocabulary service. New releases of the FOSS GeoServer application greatly improve support for complex XML feature schemas like GeoSciML, and the ArcGIS for INSPIRE extension implements similar complex feature support for ArcGIS Server. These improved server implementations greatly facilitate deploying GeoSciML services. EarthResourceML v2 adds features for information related to mining activities. SoilML provides an interchange format for soil material, soil profile, and terrain information. Work is underway to add GeoSciML to the portfolio of Open Geospatial Consortium (OGC) specifications.

Schema-driven facilitation of new hierarchy learning in the transitive inference paradigm

PubMed Central

Kumaran, Dharshan

2013-01-01

Prior knowledge, in the form of a mental schema or framework, is viewed to facilitate the learning of new information in a range of experimental and everyday scenarios. Despite rising interest in the cognitive and neural mechanisms underlying schema-driven facilitation of new learning, few paradigms have been developed to examine this issue in humans. Here we develop a multiphase experimental scenario aimed at characterizing schema-based effects in the context of a paradigm that has been very widely used across species, the transitive inference task. We show that an associative schema, comprised of prior knowledge of the rank positions of familiar items in the hierarchy, has a marked effect on transitivity performance and the development of relational knowledge of the hierarchy that cannot be accounted for by more general changes in task strategy. Further, we show that participants are capable of deploying prior knowledge to successful effect under surprising conditions (i.e., when corrective feedback is totally absent), but only when the associative schema is robust. Finally, our results provide insights into the cognitive mechanisms underlying such schema-driven effects, and suggest that new hierarchy learning in the transitive inference task can occur through a contextual transfer mechanism that exploits the structure of associative experiences. PMID:23782509

Schema-driven facilitation of new hierarchy learning in the transitive inference paradigm.

PubMed

Kumaran, Dharshan

2013-06-19

Prior knowledge, in the form of a mental schema or framework, is viewed to facilitate the learning of new information in a range of experimental and everyday scenarios. Despite rising interest in the cognitive and neural mechanisms underlying schema-driven facilitation of new learning, few paradigms have been developed to examine this issue in humans. Here we develop a multiphase experimental scenario aimed at characterizing schema-based effects in the context of a paradigm that has been very widely used across species, the transitive inference task. We show that an associative schema, comprised of prior knowledge of the rank positions of familiar items in the hierarchy, has a marked effect on transitivity performance and the development of relational knowledge of the hierarchy that cannot be accounted for by more general changes in task strategy. Further, we show that participants are capable of deploying prior knowledge to successful effect under surprising conditions (i.e., when corrective feedback is totally absent), but only when the associative schema is robust. Finally, our results provide insights into the cognitive mechanisms underlying such schema-driven effects, and suggest that new hierarchy learning in the transitive inference task can occur through a contextual transfer mechanism that exploits the structure of associative experiences.

Development of the EarthChem Geochronology and Thermochronology database: Collaboration of the EarthChem and EARTHTIME efforts

NASA Astrophysics Data System (ADS)

Walker, J. D.; Ash, J. M.; Bowring, J.; Bowring, S. A.; Deino, A. L.; Kislitsyn, R.; Koppers, A. A.

2009-12-01

One of the most onerous tasks in rigorous development of data reporting and databases for geochronological and thermochronological studies is to fully capture all of the metadata needed to completely document both the analytical work as well as the interpretation effort. This information is available in the data reduction programs used by researchers, but has proven difficult to harvest into either publications or databases. For this reason, the EarthChem and EARTHTIME efforts are collaborating to foster the next generation of data management and discovery for age information by integrating data reporting with data reduction. EarthChem is a community-driven effort to facilitate the discovery, access, and preservation of geochemical data of all types and to support research and enable new and better science. EARTHTIME is also a community-initiated project whose aim is to foster the next generation of high-precision geochronology and thermochoronology. In addition, collaboration with the CRONUS effort for cosmogenic radionuclides is in progress. EarthChem workers have met with groups working on the Ar-Ar, U-Pb, and (U-Th)/He systems to establish data reporting requirements as well as XML schemas to be used for transferring data from reduction programs to database. At present, we have prototype systems working for the U-Pb_Redux, ArArCalc, MassSpec, and Helios programs. In each program, the user can select to upload data and metadata to the GEOCHRON system hosted at EarthChem. There are two additional requirements for upload. The first is having a unique identifier (IGSN) obtained either manually or via web services contained within the reduction program from the SESAR system. The second is that the user selects whether the sample is to be available for discovery (public) or remain hidden (private). Search for data at the GEOCHRON portal can be done using age, method, mineral, or location parameters. Data can be downloaded in the full XML format for ingestion back into the reduction program or as abbreviated tables.

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.

Phased Array Excitations For Efficient Near Field Wireless Power Transmission

DTIC Science & Technology

2016-09-01

relating to the improvement of wireless - power transfer (WPT) in the near field. Improvement to power reception in the near field requires that...improvement of wireless - power transfer (WPT) in the near field. Improvement to power reception in the near field requires that excitation correction methods...transverse electromagnetic TM transverse magnetic UAV unmanned aerial vehicles VSWR voltage standing wave ratio WPT wireless power transfer XML

The new OGC Catalogue Services 3.0 specification - status of work

NASA Astrophysics Data System (ADS)

Bigagli, Lorenzo; Voges, Uwe

2013-04-01

We report on the work of the Open Geospatial Consortium Catalogue Services 3.0 Standards Working Group (OGC Cat 3.0 SWG for short), started in March 2008, with the purpose to process change requests on the Catalogue Services 2.0.2 Implementation Specification (OGC 07-006r1) and produce a revised version thereof, comprising the related XML schemas and abstract test suite. The work was initially intended as a minor revision (version 2.1), but later retargeted as a major update of the standard and rescheduled (the anticipated roadmap ended in 2008). The target audience of Catalogue Services 3.0 includes: • Implementors of catalogue services solutions. • Designers and developers of catalogue services profiles. • Providers/users of catalogue services. The two main general areas of enhancement included: restructuring the specification document according to the OGC standard for modular specifications (OGC 08-131r3, also known as Core and Extension model); incorporating the current mass-market technologies for discovery on the Web, namely OpenSearch. The document was initially split into four parts: the general model and the three protocol bindings HTTP, Z39.50, and CORBA. The CORBA binding, which was very rarely implemented, and the Z39.50 binding have later been dropped. Parts of the Z39.50 binding, namely Search/Retrieve via URL (SRU; same semantics as Z39.50, but stateless), have been provided as a discussion paper (OGC 12-082) for possibly developing a future SRU profile. The Catalogue Services 3.0 specification is structured as follows: • Part 1: General Model (Core) • Part 2: HTTP Protocol Binding (CSW) In CSW, the GET/KVP encoding is mandatory. The POST/XML encoding is optional. SOAP is supported as a special case of the POST/XML encoding. OpenSearch must always be supported, regardless of the implemented profiles, along with the OpenSearch Geospatial and Temporal Extensions (OGC 10-032r2). The latter specifies spatial (e.g. point-plus-radius, bounding box, polygons, in EPSG:4326/WGS84 coordinates) and temporal constraints (e.g. time start/end) for searching. The temporal extent (begin/end) is added as a core queryable and returnable property. Plenty of other changes are incorporated, including improvements to query distribution, WSDL and schema documents, requirements and conformance classes. In conclusion, CS 3.0 is a long-awaited revision of the previous CS 2.0.2 Implementation Specification (approved in early 2007), whose requirements started to be collected as early as July 2007. Various profiles of CS 2.0.2 exist, with related dependencies, and will need to be harmonized with this specification.

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

NASA Astrophysics Data System (ADS)

Kelbert, A.; Blum, C.

2015-12-01

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

Information Metacatalog for a Grid

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

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.

Standards for detailed clinical models as the basis for medical data exchange and decision support.

PubMed

Coyle, Joseph F; Mori, Angelo Rossi; Huff, Stanley M

2003-03-01

Detailed clinical models are necessary to exchange medical data between heterogeneous computer systems and to maintain consistency in a longitudinal electronic medical record system. At Intermountain Health Care (IHC), we have a history of designing detailed clinical models. The purpose of this paper is to share our experience and the lessons we have learned over the last 5 years. IHC's newest model is implemented using eXtensible Markup Language (XML) Schema as the formalism, and conforms to the Health Level Seven (HL7) version 3 data types. The centerpiece of the new strategy is the Clinical Event Model, which is a flexible name-value pair data structure that is tightly linked to a coded terminology. We describe IHC's third-generation strategy for representing and implementing detailed clinical models, and discuss the reasons for this design.

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

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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.

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

NASA Technical Reports Server (NTRS)

Maluf, David A.; Tran, Peter B.

2003-01-01

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

Implementation of UML Schema to RDBM

NASA Astrophysics Data System (ADS)

Nagni, M.; Ventouras, S.; Parton, G.

2012-04-01

Multiple disciplines - especially those within the earth and physical sciences, and increasingly those within social science and medical fields - require Geographic Information (GI) i.e. information concerning phenomena implicitly or explicitly associated with a location relative to the Earth [1]. Therefore geographic datasets are increasingly being shared, exchanged and frequently used for purposes other than those for which they were originally intended. The ISO Technical Committee 211 (ISO/TC 211) together with Open Geospatial Consortium (OGC) provide a series of standards and guidelines for developing application schemas which should: a) capture relevant conceptual aspects of the data involved; and b) be sufficient to satisfy previously defined use-cases of a specific or cross-domain concerns. In addition, the Hollow World technology offers an accessible and industry-standardised methodology for creating and editing Application Schema UML models which conform to international standards for interoperable GI [2]. We present a technology which seamlessly transforms an Application Schema UML model to a relational database model (RDBM). This technology, using the same UML information model, complements the XML transformation of an information model produced by the FullMoon tool [2]. In preparation for the generation of a RDBM the UML model is first mapped to a collection of OO classes and relationships. Any external dependencies that exist are then resolved through the same mechanism. However, a RDBM does not support a hierarchical (relational) data structure - a function that may be required by UML models. Previous approaches have addressed this problem through use of nested sets or an adjacent list to represent such structure. Our unique strategy addresses the hierarchical data structure issue, whether singular or multiple inheritance, by hiding a delegation pattern within an OO class. This permits the object-relational mapping (ORM) software used to generate the RDBM to easily map the class into the RDBM. In other words the particular structure of the resulting OO class may expose a "composition-like aspect" to the ORM whilst maintaining an "inherited-like aspect" for use within an OO program. This methodology has been used to implement a software application to manages the new CEDA metadata model which is based on MOLES 3.4, Python, Django and SQLAlchemy.

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.

Securely and Flexibly Sharing a Biomedical Data Management System

PubMed Central

Wang, Fusheng; Hussels, Phillip; Liu, Peiya

2011-01-01

Biomedical database systems need not only to address the issues of managing complex data, but also to provide data security and access control to the system. These include not only system level security, but also instance level access control such as access of documents, schemas, or aggregation of information. The latter is becoming more important as multiple users can share a single scientific data management system to conduct their research, while data have to be protected before they are published or IP-protected. This problem is challenging as users’ needs for data security vary dramatically from one application to another, in terms of who to share with, what resources to be shared, and at what access level. We develop a comprehensive data access framework for a biomedical data management system SciPort. SciPort provides fine-grained multi-level space based access control of resources at not only object level (documents and schemas), but also space level (resources set aggregated in a hierarchy way). Furthermore, to simplify the management of users and privileges, customizable role-based user model is developed. The access control is implemented efficiently by integrating access privileges into the backend XML database, thus efficient queries are supported. The secure access approach we take makes it possible for multiple users to share the same biomedical data management system with flexible access management and high data security. PMID:21625285

A Tsunami-Focused Tide Station Data Sharing Framework

NASA Astrophysics Data System (ADS)

Kari, U. S.; Marra, J. J.; Weinstein, S. A.

2006-12-01

The Indian Ocean Tsunami of 26 December 2004 made it clear that information about tide stations that could be used to support detection and warning (such as location, collection and transmission capabilities, operator identification) are insufficiently known or not readily accessible. Parties interested in addressing this problem united under the Pacific Region Data Integrated Data Enterprise (PRIDE), and in 2005 began a multiyear effort to develop a distributed metadata system describing tide stations starting with pilot activities in a regional framework and focusing on tsunami detection and warning systems being developed by various agencies. First, a plain semantic description of the tsunami-focused tide station metadata was developed. The semantic metadata description was, in turn, developed into a formal metadata schema championed by International Tsunami Information Centre (ITIC) as part of a larger effort to develop a prototype web service under the PRIDE program in 2005. Under the 2006 PRIDE program the formal metadata schema was then expanded to corral input parameters for the TideTool application used by Pacific Tsunami Warning Center (PTWC) to drill down into wave activity at a tide station that is located using a web service developed on this metadata schema. This effort contributed to formalization of web service dissemination of PTWC watch and warning tsunami bulletins. During this time, the data content and sharing issues embodied in this schema have been discussed at various forums. The result is that the various stakeholders have different data provider and user perspectives (semantic content) and also exchange formats (not limited to just XML). The challenge then, is not only to capture all data requirements, but also to have formal representation that is easily transformed into any specified format. The latest revision of the tide gauge schema (Version 0.3), begins to address this challenge. It encompasses a broader range of provider and user perspectives, such as station operators, warning system managers, disaster managers, other marine hazard warning systems (such as storm surges and sea level change monitoring and research. In the next revision(s), we hope to take into account various relevant standards, including specifically, the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) Framework, that will serve all prospective stakeholders in the most useful (extensible, scalable) manner. This is because Sensor ML has addressed many of the challenges we face already, through very useful fundamental modeling consideration and data types that are particular to sensors in general, with perhaps some extension needed for tide gauges. As a result of developing this schema, and associated client application architectures, we hope to have a much more distributed network of data providers, who are able to contribute to a global tide station metadata from the comfort of their own Information Technology (IT) departments.

panMetaDocs, eSciDoc, and DOIDB - an infrastructure for the curation and publication of file-based datasets for 'GFZ Data Services'

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Elger, Kirsten; Bertelmann, Roland; Klump, Jens

2016-04-01

With the foundation of DataCite in 2009 and the technical infrastructure installed in the last six years it has become very easy to create citable dataset DOIs. Nowadays, dataset DOIs are increasingly accepted and required by journals in reference lists of manuscripts. In addition, DataCite provides usage statistics [1] of assigned DOIs and offers a public search API to make research data count. By linking related information to the data, they become more useful for future generations of scientists. For this purpose, several identifier systems, as ISBN for books, ISSN for journals, DOI for articles or related data, Orcid for authors, and IGSN for physical samples can be attached to DOIs using the DataCite metadata schema [2]. While these are good preconditions to publish data, free and open solutions that help with the curation of data, the publication of research data, and the assignment of DOIs in one software seem to be rare. At GFZ Potsdam we built a modular software stack that is made of several free and open software solutions and we established 'GFZ Data Services'. 'GFZ Data Services' provides storage, a metadata editor for publication and a facility to moderate minted DOIs. All software solutions are connected through web APIs, which makes it possible to reuse and integrate established software. Core component of 'GFZ Data Services' is an eSciDoc [3] middleware that is used as central storage, and has been designed along the OAIS reference model for digital preservation. Thus, data are stored in self-contained packages that are made of binary file-based data and XML-based metadata. The eSciDoc infrastructure provides access control to data and it is able to handle half-open datasets, which is useful in embargo situations when a subset of the research data are released after an adequate period. The data exchange platform panMetaDocs [4] makes use of eSciDoc's REST API to upload file-based data into eSciDoc and uses a metadata editor [5] to annotate the files with metadata. The metadata editor has a user-friendly interface with nominal lists, extensive explanations, and an interactive mapping tool to provide assistance to scientists describing the data. It is possible to deposit metadata templates to fill certain fields with default values. The metadata editor generates metadata in the schemas ISO19139, NASA GCMD DIF, and DataCite and could be extended for other schemas. panMetaDocs is able to mint dataset DOIs through DOIDB, which is our component to moderate dataset DOIs issued through 'GFZ Data Services'. DOIDB accepts metadata in the schemas ISO19139, DIF, and DataCite. In addition, DOIDB provides an OAI-PMH interface to disseminate all deposited metadata to data portals. The presentation of datasets on DOI landing pages is done though XSLT stylesheet transformation of the XML-based metadata. The landing pages have been designed to meet needs of scientists. We are able to render the metadata to different layouts. Furthermore, additional information about datasets and publications is assembled into the webpage by querying public databases on the internet. The work presented here will focus on technical details of the software stack. [1] http://stats.datacite.org [2] http://www.dlib.org/dlib/january11/starr/01starr.html [3] http://www.escidoc.org [4] http://panmetadocs.sf.net [5] http://github.com/ulbricht

Adapt

NASA Astrophysics Data System (ADS)

Bargatze, L. F.

2015-12-01

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

Collection Metadata Solutions for Digital Library Applications

NASA Technical Reports Server (NTRS)

Hill, Linda L.; Janee, Greg; Dolin, Ron; Frew, James; Larsgaard, Mary

1999-01-01

Within a digital library, collections may range from an ad hoc set of objects that serve a temporary purpose to established library collections intended to persist through time. The objects in these collections vary widely, from library and data center holdings to pointers to real-world objects, such as geographic places, and the various metadata schemas that describe them. The key to integrated use of such a variety of collections in a digital library is collection metadata that represents the inherent and contextual characteristics of a collection. The Alexandria Digital Library (ADL) Project has designed and implemented collection metadata for several purposes: in XML form, the collection metadata "registers" the collection with the user interface client; in HTML form, it is used for user documentation; eventually, it will be used to describe the collection to network search agents; and it is used for internal collection management, including mapping the object metadata attributes to the common search parameters of the system.

Enabling private and public sector organizations as agents of homeland security

NASA Astrophysics Data System (ADS)

Glassco, David H. J.; Glassco, Jordan C.

2006-05-01

Homeland security and defense applications seek to reduce the risk of undesirable eventualities across physical space in real-time. With that functional requirement in mind, our work focused on the development of IP based agent telecommunication solutions for heterogeneous sensor / robotic intelligent "Things" that could be deployed across the internet. This paper explains how multi-organization information and device sharing alliances may be formed to enable organizations to act as agents of homeland security (in addition to other uses). Topics include: (i) using location-aware, agent based, real-time information sharing systems to integrate business systems, mobile devices, sensor and actuator based devices and embedded devices used in physical infrastructure assets, equipment and other man-made "Things"; (ii) organization-centric real-time information sharing spaces using on-demand XML schema formatted networks; (iii) object-oriented XML serialization as a methodology for heterogeneous device glue code; (iv) how complex requirements for inter / intra organization information and device ownership and sharing, security and access control, mobility and remote communication service, tailored solution life cycle management, service QoS, service and geographic scalability and the projection of remote physical presence (through sensing and robotics) and remote informational presence (knowledge of what is going elsewhere) can be more easily supported through feature inheritance with a rapid agent system development methodology; (v) how remote object identification and tracking can be supported across large areas; (vi) how agent synergy may be leveraged with analytics to complement heterogeneous device networks.

An Adaptable Seismic Data Format for Modern Scientific Workflows

NASA Astrophysics Data System (ADS)

Smith, J. A.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Podhorszki, N.; Tromp, J.

2013-12-01

Data storage, exchange, and access play a critical role in modern seismology. Current seismic data formats, such as SEED, SAC, and SEG-Y, were designed with specific applications in mind and are frequently a major bottleneck in implementing efficient workflows. We propose a new modern parallel format that can be adapted for a variety of seismic workflows. The Adaptable Seismic Data Format (ASDF) features high-performance parallel read and write support and the ability to store an arbitrary number of traces of varying sizes. Provenance information is stored inside the file so that users know the origin of the data as well as the precise operations that have been applied to the waveforms. The design of the new format is based on several real-world use cases, including earthquake seismology and seismic interferometry. The metadata is based on the proven XML schemas StationXML and QuakeML. Existing time-series analysis tool-kits are easily interfaced with this new format so that seismologists can use robust, previously developed software packages, such as ObsPy and the SAC library. ADIOS, netCDF4, and HDF5 can be used as the underlying container format. At Princeton University, we have chosen to use ADIOS as the container format because it has shown superior scalability for certain applications, such as dealing with big data on HPC systems. In the context of high-performance computing, we have implemented ASDF into the global adjoint tomography workflow on Oak Ridge National Laboratory's supercomputer Titan.

A Simple XML Producer-Consumer Protocol

NASA Technical Reports Server (NTRS)

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

2001-01-01

There are many different projects from government, academia, and industry that provide services for delivering events in distributed environments. The problem with these event services is that they are not general enough to support all uses and they speak different protocols so that they cannot interoperate. We require such interoperability when we, for example, wish to analyze the performance of an application in a distributed environment. Such an analysis might require performance information from the application, computer systems, networks, and scientific instruments. In this work we propose and evaluate a standard XML-based protocol for the transmission of events in distributed systems. One recent trend in government and academic research is the development and deployment of computational grids. Computational grids are large-scale distributed systems that typically consist of high-performance compute, storage, and networking resources. Examples of such computational grids are the DOE Science Grid, the NASA Information Power Grid (IPG), and the NSF Partnerships for Advanced Computing Infrastructure (PACIs). The major effort to deploy these grids is in the area of developing the software services to allow users to execute applications on these large and diverse sets of resources. These services include security, execution of remote applications, managing remote data, access to information about resources and services, and so on. There are several toolkits for providing these services such as Globus, Legion, and Condor. As part of these efforts to develop computational grids, the Global Grid Forum is working to standardize the protocols and APIs used by various grid services. This standardization will allow interoperability between the client and server software of the toolkits that are providing the grid services. The goal of the Performance Working Group of the Grid Forum is to standardize protocols and representations related to the storage and distribution of performance data. These standard protocols and representations must support tasks such as profiling parallel applications, monitoring the status of computers and networks, and monitoring the performance of services provided by a computational grid. This paper describes a proposed protocol and data representation for the exchange of events in a distributed system. The protocol exchanges messages formatted in XML and it can be layered atop any low-level communication protocol such as TCP or UDP Further, we describe Java and C++ implementations of this protocol and discuss their performance. The next section will provide some further background information. Section 3 describes the main communication patterns of our protocol. Section 4 describes how we represent events and related information using XML. Section 5 describes our protocol and Section 6 discusses the performance of two implementations of the protocol. Finally, an appendix provides the XML Schema definition of our protocol and event information.

Metadata and Service at the GFZ ISDC Portal

NASA Astrophysics Data System (ADS)

Ritschel, B.

2008-05-01

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

Preparing Laboratory and Real-World EEG Data for Large-Scale Analysis: A Containerized Approach

PubMed Central

Bigdely-Shamlo, Nima; Makeig, Scott; Robbins, Kay A.

2016-01-01

Large-scale analysis of EEG and other physiological measures promises new insights into brain processes and more accurate and robust brain–computer interface models. However, the absence of standardized vocabularies for annotating events in a machine understandable manner, the welter of collection-specific data organizations, the difficulty in moving data across processing platforms, and the unavailability of agreed-upon standards for preprocessing have prevented large-scale analyses of EEG. Here we describe a “containerized” approach and freely available tools we have developed to facilitate the process of annotating, packaging, and preprocessing EEG data collections to enable data sharing, archiving, large-scale machine learning/data mining and (meta-)analysis. The EEG Study Schema (ESS) comprises three data “Levels,” each with its own XML-document schema and file/folder convention, plus a standardized (PREP) pipeline to move raw (Data Level 1) data to a basic preprocessed state (Data Level 2) suitable for application of a large class of EEG analysis methods. Researchers can ship a study as a single unit and operate on its data using a standardized interface. ESS does not require a central database and provides all the metadata data necessary to execute a wide variety of EEG processing pipelines. The primary focus of ESS is automated in-depth analysis and meta-analysis EEG studies. However, ESS can also encapsulate meta-information for the other modalities such as eye tracking, that are increasingly used in both laboratory and real-world neuroimaging. ESS schema and tools are freely available at www.eegstudy.org and a central catalog of over 850 GB of existing data in ESS format is available at studycatalog.org. These tools and resources are part of a larger effort to enable data sharing at sufficient scale for researchers to engage in truly large-scale EEG analysis and data mining (BigEEG.org). PMID:27014048

Narrowing the Transfer Gap: The Advantages of "as if" Situations in Training.

ERIC Educational Resources Information Center

Vermeulen, Rita C. M.

2002-01-01

A schema a frame creates context and shapes interpretation. Using an "as if" framework can connect the contexts of training and job performance to improve transfer. Techniques that create "as if" situations include role playing, visualization, psychodrama, voice dialogue, improvisation, playback theatre, and six-steps reframing. (Contains 23…

CISN Display Progress to Date - Reliable Delivery of Real-Time Earthquake Information, and ShakeMap to Critical End Users

NASA Astrophysics Data System (ADS)

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

2003-12-01

The California Integrated Seismic Network (CISN) has collaborated to develop a next-generation earthquake notification system that is nearing its first operations-ready release. The CISN Display actively alerts users of seismic data, and vital earthquake hazards information following a significant event. It will primarily replace the Caltech/USGS Broadcast of Earthquakes (CUBE) and Rapid Earthquake Data Integration (REDI) Display as the principal means of delivering geographical seismic data to emergency operations centers, utility companies and media outlets. A subsequent goal is to provide automated access to the many Web products produced by regional seismic networks after an earthquake. Another aim is to create a highly configurable client, allowing user organizations to overlay infrastructure data critical to their roles as first-responders, or lifeline operators. And the final goal is to integrate these requirements, into a package offering several layers of reliability to ensure delivery of services. Central to the CISN Display's role as a gateway to Web-based earthquake products is its comprehensive XML-messaging schema. The message model uses many of the same attributes in the CUBE format, but extends the old standard by provisioning additional elements for products currently available, and others yet to be considered. The client consumes these XML-messages, sorts them through a resident Quake Data Merge filter, and posts updates that also include hyperlinks associated to specific event IDs on the display map. Earthquake products available for delivery to the CISN Display are ShakeMap, focal mechanisms, waveform data, felt reports, aftershock forecasts and earthquake commentaries. By design the XML-message schema can evolve as products and information needs change, without breaking existing applications that rely on it. The latest version of the CISN Display can also automatically download ShakeMaps and display shaking intensity within the GIS system. This can give Emergency Response managers' information needed to allocate limited personnel and resources after a major event. The shaking intensity shape files may be downloaded out-of-band to the client computer, and with the GIS mapping tool, users can plot organizational assets on the CISN Display map and analyze their inventory against potentially damaged areas. Lastly, in support of a robust design is a well-established and reliable set of communication protocols. To achieve a state-full server connection and messaging via a signaling channel the application uses a Common Object Request Broker Architecture (CORBA). The client responds to keep-alive signals from the server, and alerts users of changes in the connection status. This full-featured messaging service will allow the system to trigger a reconnect strategy whenever the client detects a loss of connectivity. This sets the CISN Display apart from its predecessors, which do not provide a failover mechanism, or a state of connection. Thus by building on past programming successes and advances in proven Internet technologies, the CISN Display will augment the emergency responder's ability to make informed decisions following a potentially damaging earthquake.

Achieving interoperability for metadata registries using comparative object modeling.

PubMed

Park, Yu Rang; Kim, Ju Han

2010-01-01

Achieving data interoperability between organizations relies upon agreed meaning and representation (metadata) of data. For managing and registering metadata, many organizations have built metadata registries (MDRs) in various domains based on international standard for MDR framework, ISO/IEC 11179. Following this trend, two pubic MDRs in biomedical domain have been created, United States Health Information Knowledgebase (USHIK) and cancer Data Standards Registry and Repository (caDSR), from U.S. Department of Health & Human Services and National Cancer Institute (NCI), respectively. Most MDRs are implemented with indiscriminate extending for satisfying organization-specific needs and solving semantic and structural limitation of ISO/IEC 11179. As a result it is difficult to address interoperability among multiple MDRs. In this paper, we propose an integrated metadata object model for achieving interoperability among multiple MDRs. To evaluate this model, we developed an XML Schema Definition (XSD)-based metadata exchange format. We created an XSD-based metadata exporter, supporting both the integrated metadata object model and organization-specific MDR formats.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

Utilizing the International GeoSample Number Concept during ICDP Expedition COSC

NASA Astrophysics Data System (ADS)

Conze, Ronald; Lorenz, Henning; Ulbricht, Damian; Gorgas, Thomas; Elger, Kirsten

2016-04-01

The concept of the International GeoSample Number (IGSN) was introduced to uniquely identify and register geo-related sample material, and make it retrievable via electronic media (e.g., SESAR - http://www.geosamples.org/igsnabout). The general aim of the IGSN concept is to improve accessing stored sample material worldwide, enable the exact identification, its origin and provenance, and also the exact and complete citation of acquired samples throughout the literature. The ICDP expedition COSC (Collisional Orogeny in the Scandinavian Caledonides, http://cosc.icdp-online.org) prompted for the first time in ICDP's history to assign and register IGSNs during an ongoing drilling campaign. ICDP drilling expeditions are using commonly the Drilling Information System DIS (http://doi.org/10.2204/iodp.sd.4.07.2007) for the inventory of recovered sample material. During COSC IGSNs were assigned to every drill hole, core run, core section, and sample taken from core material. The original IGSN specification has been extended to achieve the required uniqueness of IGSNs with our offline-procedure. The ICDP name space indicator and the Expedition ID (5054) are forming an extended prefix (ICDP5054). For every type of sample material, an encoded sequence of characters follows. This sequence is derived from the DIS naming convention which is unique from the beginning. Thereby every ICDP expedition has an unlimited name space for IGSN assignments. This direct derivation of IGSNs from the DIS database context ensures the distinct parent-child hierarchy of the IGSNs among each other. In the case of COSC this method of inventory-keeping of all drill cores was done routinely using the ExpeditionDIS during field work and subsequent sampling party. After completing the field campaign, all sample material was transferred to the "Nationales Bohrkernlager" in Berlin-Spandau, Germany. Corresponding data was subsequently imported into the CurationDIS used at the aforementioned core storage facility. This CurationDIS assigns IGSNs on samples newly taken in the repository in the identical fashion as done in the field. Thereby, the parent-child linkage of the IGSNs is ensured consistently throughout the entire sampling process. The only difference between ExpeditionDIS and CurationDIS sample curation is using the name space ICDP and BGRB respectively as part of the corresponding ID string. To prepare the IGSN registry, a set of metadata is generated for every assigned IGSN using the DIS, which is then exported from the DIS into one common xml-file. The xml-file is based on the SESAR schema and a proposal of IGSN e.V. (http://schema.igsn.org). This systematics has been recently extended for drilling data to achieve additional information for future retrieval options. The two allocation agents GFZ Potsdam und PANGAEA are currently involved in the registry of IGSNs in the case of COSC drill campaigns. An example for the IGSN registration of the COSC-1 drill hole A (5054_1_A) is "ICDP5054EEW1001" and can be resolved using the URL http://hdl.handle.net/10273/ICDP5054EEW1001. Opening the landing page for the complete COSC core material for this particular hole showcases graphically a hierarchical tree entitled "Sample Family". An example of an IGSN citation associated with a COSC sample set is featured on an EGU-2016 poster presentation by Ulrich Harms, Johannes Hierold et al. (EGU2016-8646).

InterMine Webservices for Phytozome (Rev2)

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

Carlson, Joseph; Goodstein, David; Rokhsar, Dan

2014-07-10

A datawarehousing framework for information provides a useful infrastructure for providers and users of genomic data. For providers, the infrastructure give them a consistent mechanism for extracting raw data. While for the users, the web services supported by the software allows them to make complex, and often unique, queries of the data. Previously, phytozome.net used BioMart to provide the infrastructure. As the complexity, scale and diversity of the dataset as grown, we decided to implement an InterMine web service on our servers. This change was largely motivated by the ability to have a more complex table structure and richer webmore » reporting mechanism than BioMart. For InterMine to achieve its more complex database schema it requires an XML description of the data and an appropriate loader. Unlimited one-to-many and many-to-many relationship between the tables can be enabled in the schema. We have implemented support for:1.) Genomes and annotations for the data in Phytozome. This set is the 48 organisms currently stored in a back end CHADO datastore. The data loaders are modified versions of the CHADO data adapters from FlyMine. 2.) Interproscan results from all proteins in the Phytozome database. 3.) Clusters of proteins into a grouped heirarchically by similarity. 4.) Cufflinks results from tissue-specific RNA-Seq data of Phytozome organisms. 5.) Diversity data (GATK and SnpEFF results) from a set of individual organism. The last two datatypes are new in this implementation of our web services. We anticipate that the scale of these data will increase considerably in the near future.« less

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

NASA Astrophysics Data System (ADS)

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

2005-05-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Speed up of XML parsers with PHP language implementation

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2012-11-01

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

Development of Extended Content Standards for Biodiversity Data

NASA Astrophysics Data System (ADS)

Hugo, Wim; Schmidt, Jochen; Saarenmaa, Hannu

2013-04-01

Interoperability in the field of Biodiversity observation has been strongly driven by the development of a number of global initiatives (GEO, GBIF, OGC, TDWG, GenBank, …) and its supporting standards (OGC-WxS, OGC-SOS, Darwin Core (DwC), NetCDF, …). To a large extent, these initiatives have focused on discoverability and standardization of syntactic and schematic interoperability. Semantic interoperability is more complex, requiring development of domain-dependent conceptual data models, and extension of these models with appropriate ontologies (typically manifested as controlled vocabularies). Biodiversity content has been standardized partly, for example through Darwin Core for occurrence data and associated taxonomy, and through Genbank for genetic data, but other contexts of biodiversity observation have lagged behind - making it difficult to achieve semantic interoperability between distributed data sources. With this in mind, WG8 of GEO BON (charged with data and systems interoperability) has started a work programme to address a number of concerns, one of which is the gap in content standards required to make Biodiversity data truly interoperable. The paper reports on the framework developed by WG8 for the classification of Biodiversity observation data into 'families' of use cases and its supporting data schema, where gaps, if any, in the availability if content standards have been identified, and how these are to be addressed by way of an abstract data model and the development of associated content standards. It is proposed that a minimum set of standards (1) will be required to address the scope of Biodiversity content, aligned with levels and dimensions of observation, and based on the 'Essential Biodiversity Variables' (2) being developed by GEO BON . The content standards are envisaged as loosely separated from the syntactic and schematic standards used for the base data exchange: typically, services would offer an existing data standard (DwC, WFS, SOS, NetCDF), with a use-case dependent 'payload' embedded into the data stream. This enables the re-use of the abstract schema, and sometimes the implementation specification (for example XML, JSON, or NetCDF conventions) across services. An explicit aim will be to make the XML implementation specification re-usable as a DwC and a GML (SOS end WFS) extension. (1) Olga Lyashevska, Keith D. Farnsworth, How many dimensions of biodiversity do we need?, Ecological Indicators, Volume 18, July 2012, Pages 485-492, ISSN 1470-160X, 10.1016/j.ecolind.2011.12.016. (2) GEO BON: Workshop on Essential Biodiversity Variables (27-29 February 2012, Frascati, Italy). (http://www.earthobservations.org/geobon_docs_20120227.shtml)

Enabling conformity to international standards within SeaDataNet

NASA Astrophysics Data System (ADS)

Schaap, Dick M. A.; Boldrini, Enrico; de Korte, Arjen; Santoro, Mattia; Manzella, Giuseppe; Nativi, Stefano

2010-05-01

SeaDataNet objective is to construct a standardized system for managing the large and diverse data sets collected by the oceanographic fleets and the new automatic observation systems. The aim is to network and enhance the currently existing infrastructures, which are the national oceanographic data centres and satellite data centres of 36 countries, active in data collection. The networking of these professional data centres, in a unique virtual data management system will provide integrated data sets of standardized quality on-line. The Common Data Index (CDI) is the middleware service adopted by SeaDataNet for discovery and access of the available data. In order to develop an interoperable and effective system, the use of international de facto and de jure standards is required. In particular the new goal object of this presentation is to introduce and discuss the solutions for making SeaDataNet compliant with the European Union (EU) INSPIRE directive and in particular with its Implementing Rules (IR). The European INSPIRE directive aims to rule the creation of an European Spatial Data Infrastructure (ESDI). This will enable the sharing of environmental spatial information among public sector organisations and better facilitate public access to spatial information across Europe. To ensure that the spatial data infrastructures of the European Member States are compatible and usable in a community and transboundary context, the directive requires that common IRs are adopted in a number of specific areas (Metadata, Data Specifications, Network Services, Data and Service Sharing and Monitoring and Reporting). Often the use of already approved digital geographic information standards is mandated, drawing from international organizations like the Open Geospatial Consortium (OGC) and the International Organization for Standardization (ISO), the latter by means of its Technical Committee 211 (ISO/TC 211). In the context of geographic data discovery a set of mandatory metadata information is identified by INSPIRE metadata regulations and recommended implementations appear in IRs, in particular the use of ISO 19139 Application Profile (ISO AP) of OGC Catalogue Service for the Web 2.0.2 (CSW), as well as the use of ISO19139 XML schemas (along with additional constraints) to encode and distribute the required INSPIRE metadata. SeaDataNet started its work in 2006, basing its metadata schema upon the ISO 19115 DTD, the available schema at that time. Overtime this was replaced with the present CDI v.1 XML schema, based on ISO 19115 abstract model with community specific features and constraints. In order to assure the INSPIRE conformity a GI-cat based solution was developed. GI-cat is a broker service able to mediate from different metadata sources and publish them through a consistent and unified interface. In this case GI-cat is used as a front end to the SeaDataNet portal publishing the available data, based on CDI v.1, through a CSW AP ISO interface. The first step consisted in the precise definition of a community profile of ISO19115, containing both INSPIRE and CDI driven constraints and extensions. This abstract model is ready to be implemented both in CDI v.1 and in ISO 19139; to this aim, guidelines were drafted. Then a mapping from the CDI v.1 to the ISO 19139 implementation was ready to be produced. The work resulted in the creation of a new CDI accessor within GI-cat. These type of components play the role of data model mediators within the framework. While a replacement of the CDI v.1 format with the ISO 19139 solution is planned for SeaDataNet in the future, this front-end solution make data discovery readily effective by clients within the INSPIRE community.

Using SWE Standards for Ubiquitous Environmental Sensing: A Performance Analysis

PubMed Central

Tamayo, Alain; Granell, Carlos; Huerta, Joaquín

2012-01-01

Although smartphone applications represent the most typical data consumer tool from the citizen perspective in environmental applications, they can also be used for in-situ data collection and production in varied scenarios, such as geological sciences and biodiversity. The use of standard protocols, such as SWE, to exchange information between smartphones and sensor infrastructures brings benefits such as interoperability and scalability, but their reliance on XML is a potential problem when large volumes of data are transferred, due to limited bandwidth and processing capabilities on mobile phones. In this article we present a performance analysis about the use of SWE standards in smartphone applications to consume and produce environmental sensor data, analysing to what extent the performance problems related to XML can be alleviated by using alternative uncompressed and compressed formats.

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…

78 FR 70954 - Transport Format for the Submission of Regulatory Study Data; Notice of Pilot Project

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-27

... extensible modern technology. SDS XML is an extension of the CDISC Operational Data Model, which is a vendor... many to be an outdated transport technology for transferring data across different hardware and... public meeting was to solicit input from industry, technology vendors, and other members of the public...

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.

PubMed

Sanderson, Lacey-Anne; Ficklin, Stephen P; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A; Bett, Kirstin E; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

PubMed Central

Sanderson, Lacey-Anne; Ficklin, Stephen P.; Cheng, Chun-Huai; Jung, Sook; Feltus, Frank A.; Bett, Kirstin E.; Main, Dorrie

2013-01-01

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map’, ‘Genetic’, ‘Publication’, ‘Project’, ‘Contact’ and the ‘Natural Diversity’ modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. Database URL: http://tripal.info/ PMID:24163125

The Planetary Data System Information Model for Geometry Metadata

NASA Astrophysics Data System (ADS)

Guinness, E. A.; Gordon, M. K.

2014-12-01

The NASA Planetary Data System (PDS) has recently developed a new set of archiving standards based on a rigorously defined information model. An important part of the new PDS information model is the model for geometry metadata, which includes, for example, attributes of the lighting and viewing angles of observations, position and velocity vectors of a spacecraft relative to Sun and observing body at the time of observation and the location and orientation of an observation on the target. The PDS geometry model is based on requirements gathered from the planetary research community, data producers, and software engineers who build search tools. A key requirement for the model is that it fully supports the breadth of PDS archives that include a wide range of data types from missions and instruments observing many types of solar system bodies such as planets, ring systems, and smaller bodies (moons, comets, and asteroids). Thus, important design aspects of the geometry model are that it standardizes the definition of the geometry attributes and provides consistency of geometry metadata across planetary science disciplines. The model specification also includes parameters so that the context of values can be unambiguously interpreted. For example, the reference frame used for specifying geographic locations on a planetary body is explicitly included with the other geometry metadata parameters. The structure and content of the new PDS geometry model is designed to enable both science analysis and efficient development of search tools. The geometry model is implemented in XML, as is the main PDS information model, and uses XML schema for validation. The initial version of the geometry model is focused on geometry for remote sensing observations conducted by flyby and orbiting spacecraft. Future releases of the PDS geometry model will be expanded to include metadata for landed and rover spacecraft.

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

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.

A Model-Driven, Science Data Product Registration Service

NASA Astrophysics Data System (ADS)

Hardman, S.; Ramirez, P.; Hughes, J. S.; Joyner, R.; Cayanan, M.; Lee, H.; Crichton, D. J.

2011-12-01

The Planetary Data System (PDS) has undertaken an effort to overhaul the PDS data architecture (including the data model, data structures, data dictionary, etc.) and to deploy an upgraded software system (including data services, distributed data catalog, etc.) that fully embraces the PDS federation as an integrated system while taking advantage of modern innovations in information technology (including networking capabilities, processing speeds, and software breakthroughs). A core component of this new system is the Registry Service that will provide functionality for tracking, auditing, locating, and maintaining artifacts within the system. These artifacts can range from data files and label files, schemas, dictionary definitions for objects and elements, documents, services, etc. This service offers a single reference implementation of the registry capabilities detailed in the Consultative Committee for Space Data Systems (CCSDS) Registry Reference Model White Book. The CCSDS Reference Model in turn relies heavily on the Electronic Business using eXtensible Markup Language (ebXML) standards for registry services and the registry information model, managed by the OASIS consortium. Registries are pervasive components in most information systems. For example, data dictionaries, service registries, LDAP directory services, and even databases provide registry-like services. These all include an account of informational items that are used in large-scale information systems ranging from data values such as names and codes, to vocabularies, services and software components. The problem is that many of these registry-like services were designed with their own data models associated with the specific type of artifact they track. Additionally these services each have their own specific interface for interacting with the service. This Registry Service implements the data model specified in the ebXML Registry Information Model (RIM) specification that supports the various artifacts above as well as offering the flexibility to support customer-defined artifacts. Key features for the Registry Service include: - Model-based configuration specifying customer-defined artifact types, metadata attributes to capture for each artifact type, supported associations and classification schemes. - A REST-based external interface that is accessible via the Hypertext Transfer Protocol (HTTP). - Federation of Registry Service instances allowing associations between registered artifacts across registries as well as queries for artifacts across those same registries. A federation also enables features such as replication and synchronization if desired for a given deployment. In addition to its use as a core component of the PDS, the generic implementation of the Registry Service facilitates its applicability as a core component in any science data archive or science data system.

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

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

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

2006-01-01

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

Towards a theoretical clarification of biomimetics using conceptual tools from engineering design.

PubMed

Drack, M; Limpinsel, M; de Bruyn, G; Nebelsick, J H; Betz, O

2017-12-13

Many successful examples of biomimetic products are available, and most research efforts in this emerging field are directed towards the development of specific applications. The theoretical and conceptual underpinnings of the knowledge transfer between biologists, engineers and architects are, however, poorly investigated. The present article addresses this gap. We use a 'technomorphic' approach, i.e. the application of conceptual tools derived from engineering design, to better understand the processes operating during a typical biomimetic research project. This helps to elucidate the formal connections between functions, working principles and constructions (in a broad sense)-because the 'form-function-relationship' is a recurring issue in biology and engineering. The presented schema also serves as a conceptual framework that can be implemented for future biomimetic projects. The concepts of 'function' and 'working principle' are identified as the core elements in the biomimetic knowledge transfer towards applications. This schema not only facilitates the development of a common language in the emerging science of biomimetics, but also promotes the interdisciplinary dialogue among its subdisciplines.

Definition of a CDI metadata profile and its ISO 19139 based encoding

NASA Astrophysics Data System (ADS)

Boldrini, Enrico; de Korte, Arjen; Santoro, Mattia; Schaap, Dick M. A.; Nativi, Stefano; Manzella, Giuseppe

2010-05-01

The Common Data Index (CDI) is the middleware service adopted by SeaDataNet for discovery and query. The primary goal of the EU funded project SeaDataNet is to develop a system which provides transparent access to marine data sets and data products from 36 countries in and around Europe. The European context of SeaDataNet requires that the developed system complies with European Directive INSPIRE. In order to assure the required conformity a GI-cat based solution is proposed. GI-cat is a broker service able to mediate from different metadata sources and publish them through a consistent and unified interface. In this case GI-cat is used as a front end to the SeaDataNet portal publishing the original data, based on CDI v.1 XML schema, through an ISO 19139 application profile catalog interface (OGC CSW AP ISO). The choice of ISO 19139 is supported and driven by INSPIRE Implementing Rules, that have been used as a reference through the whole development process. A mapping from the CDI data model to the ISO 19139 was hence to be implemented in GI-cat and a first draft quickly developed, as both CDI v.1 and ISO 19139 happen to be XML implementations based on the same abstract data model (standard ISO 19115 - metadata about geographic information). This first draft mapping pointed out the CDI metadata model differences with respect to ISO 19115, as it was not possible to accommodate all the information contained in CDI v.1 into ISO 19139. Moreover some modifications were needed in order to reach INSPIRE compliance. The consequent work consisted in the definition of the CDI metadata model as a profile of ISO 19115. This included checking of all the metadata elements present in CDI and their cardinality. A comparison was made with respect to ISO 19115 and possible extensions were individuated. ISO 19139 was then chosen as a natural XML implementation of this new CDI metadata profile. The mapping and the profile definition processes were iteratively refined leading up to a complete mapping from the CDI data model to ISO 19139. Several issues were faced during the definition process. Among these: dynamic lists and vocabularies used by SeaDataNet could not be easily accommodated in ISO 19139, time resolution information from CDI v.1 was also difficult to accommodate, ambiguities both in the ISO 19139 specification and in the INSPIRE regulations (e.g. regarding to the bounding polygon, the language and the role of the responsible party). Another outcome of this process is the set up of conventions regarding the protocol formats to be used for a useful machine to machine data access. Changes to the original ISO 19139 schema were at the maximum extent avoided because of practical reasons within SeaDataNet: additional constraint required by the profile have been defined and will be checked by the use of Schematron or other validation mechanisms. The achieved mapping was finally ready to be integrated in GI-cat by implementation of a new accessor component for CDI. These type of components play the role of data model mediators within GI-cat framework. The new defined profile and its implementation will also be used within SeaDataNet as a replacement of the current data model implementation (CDI v.1).

Second Language Listening Comprehension: A Schema-Theoretic Perspective.

ERIC Educational Resources Information Center

Long, Donna Reseigh

1989-01-01

Enormous potential exists for the transfer of listening comprehension theory to second language listening research. The need for such research is highlighted through an exploration of recurring themes in the literature on background knowledge and through application of these themes to second language listening comprehension. (CB)

An Interface Transformation Strategy for AF-IPPS

DTIC Science & Technology

2012-12-01

Representational State Transfer (REST) and Java Enterprise Edition ( Java EE) to implement a reusable “translation service.” For SOAP and REST protocols, XML and...of best-of-breed open source software. The product baseline is summarized in the following table: Product Function Description Java Language...Compiler & Runtime JBoss Application Server Applications, Messaging, Translation Java EE Application Server Ruby on Rails Applications Ruby Web

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.

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.

Design Drivers of Water Data Services

NASA Astrophysics Data System (ADS)

Valentine, D.; Zaslavsky, I.

2008-12-01

The CUAHSI Hydrologic Information System (HIS) is being developed as a geographically distributed network of hydrologic data sources and functions that are integrated using web services so that they function as a connected whole. The core of the HIS service-oriented architecture is a collection of water web services, which provide uniform access to multiple repositories of observation data. These services use SOAP protocols communicating WaterML (Water Markup Language). When a client makes a data or metadata request using a CUAHSI HIS web service, these requests are made in standard manner, following the CUAHSI HIS web service signatures - regardless of how the underlying data source may be organized. Also, regardless of the format in which the data are returned by the source, the web services respond to requests by returning the data in a standard format of WaterML. The goal of WaterML design has been to capture semantics of hydrologic observations discovery and retrieval and express the point observations information model as an XML schema. To a large extent, it follows the representation of the information model as adopted by the CUASHI Observations Data Model (ODM) relational design. Another driver of WaterML design is specifications and metadata adopted by USGS NWIS, EPA STORET, and other federal agencies, as it seeks to provide a common foundation for exchanging both agency data and data collected in multiple academic projects. Another WaterML design principle was to create, in version 1 of HIS in particular, a fairly rigid and simple XML schema which is easy to generate and parse, thus creating the least barrier for adoption by hydrologists. WaterML includes a series of elements that reflect common notions used in describing hydrologic observations, such as site, variable, source, observation series, seriesCatalog, and data values. Each of the three main request methods in the water web services - GetSiteInfo, GetVariableInfo, and GetValues - has a corresponding response element in WaterML: SitesResponse, VariableResponse, and TimeSeriesResponse. The WaterML specification is being adopted by federal agencies. The experimental USGS NWIS Daily Values web service returns WaterML-compliant TImeSeriesResponse. The National Climatic Data Center is also prototyping WaterML for data delivery, and has developed a REST-based service that generates WaterML- compliant output for the NCDC ASOS network. Such agency-supported web services coming online provide a much more efficient way to deliver agency data compared to the web site scraper services that the CUAHSI HIS project has developed initially. The CUAHSI water data web services will continue to serve as the main communication mechanism within CUAHSI HIS, connecting a variety of data sources with a growing set of web service clients being developed in both academia and the commercial sector. The driving forces for the development of web services continue to be: - Application experience and needs of the growing number of CUAHSI HIS users, who experiment with additional data types, analysis modes, data browsing and searching strategies, and provide feedback to WaterML developers; - Data description requirements posed by various federal and state agencies; - Harmonization with standards being adopted or developed in neighboring communities, in particular the relevant standards being explored within the Open Geospatial Consortium. CUAHSI WaterML is a standard output schema for CUAHSI HIS water web services. Its formal specification is available as OGC discussion paper at www.opengeospatial.org/standards/dp/ class="ab'>

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

A Measurement Model of Microgenetic Transfer for Improving Instructional Outcomes

ERIC Educational Resources Information Center

Pavlik, Philip I., Jr.; Yudelson, Michael; Koedinger, Kenneth R.

2015-01-01

Efforts to improve instructional task design often make reference to the mental structures, such as "schemas" (e.g., Gick & Holyoak, 1983) or "identical elements" (Thorndike & Woodworth, 1901), that are common to both the instructional and target tasks. This component based (e.g., Singley & Anderson, 1989) approach…

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

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.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

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.

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.

RecPhyloXML - a format for reconciled gene trees.

PubMed

Duchemin, Wandrille; Gence, Guillaume; Arigon Chifolleau, Anne-Muriel; Arvestad, Lars; Bansal, Mukul S; Berry, Vincent; Boussau, Bastien; Chevenet, François; Comte, Nicolas; Davín, Adrián A; Dessimoz, Christophe; Dylus, David; Hasic, Damir; Mallo, Diego; Planel, Rémi; Posada, David; Scornavacca, Celine; Szöllosi, Gergely; Zhang, Louxin; Tannier, Éric; Daubin, Vincent

2018-05-14

A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. http://phylariane.univ-lyon1.fr/recphyloxml/. wandrille.duchemin@univ-lyon1.fr. There is no supplementary data associated with this publication.

Telemetry Attributes Transfer Standard (TMATS) Handbook

DTIC Science & Technology

2017-01-01

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

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.

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…

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.

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.

Unusual hand postures but not familiar tools show motor equivalence with precision grasping.

PubMed

Tang, Rixin; Whitwell, Robert L; Goodale, Melvyn A

2016-06-01

A central question in sensorimotor control is whether or not actions performed with the hands and corresponding actions performed with tools share a common underlying motor plan, even though different muscles and effectors are engaged. There is certainly evidence that tools used to extend the reach of the limb can be incorporated into the body schema after training. But even so, it is not clear whether or not actions such as grasping with tools and grasping with the fingers share the same programming network, i.e. show 'motor equivalence'. Here we first show that feedback-appropriate motor programming for grasps with atypical hand postures readily transfers to stereotypical precision grasps. In stark contrast, however, we find no evidence for an analogous transfer of the programming for grasps using tools to the same stereotypical precision grasps. These findings have important implications for our understanding of body schema. Although the extension of the limb that is afforded by tool use may be incorporated into the body schema, the programming of a grasping movement made with tools appears to resist such incorporation. It could be the case that the proprioceptive signals from the limb can be easily updated to reflect the end of a tool held in the hand, but the motor programs and sensory signals associated with grasping with the thumb and finger cannot be easily adapted to control the opening and closing of a tool. Instead, new but well-practiced motor programs are put in place for tool use that do not exhibit motor equivalence with manual grasping. Copyright © 2016 Elsevier B.V. All rights reserved.

XML Files

MedlinePlus

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Wireless energy transfer: Dielectric lens antennas for beam shaping in wireless power-transfer applications

NASA Astrophysics Data System (ADS)

Gonçalves, Ricardo; Carvalho, Nuno B.; Pinho, Pedro

2017-02-01

In the current contest of wireless systems, the last frontier remains the cut of the power cord. In that sense, the interest over wireless energy transfer technologies in the past years has grown exponentially. However, there are still many challenges to be overcome in order to enable wireless energy transfer full potential. One of the focus in the development of such systems is the design of very-high-gain, highly efficient, antennas that can compensate for the propagation loss of radio signals over the air. In this paper, we explore the design and manufacturing process of dielectric lenses, fabricated using a professional-grade desktop 3D printer. Lens antennas are used in order to increase beam efficiency and therefore maximize the efficiency of a wireless power-transfer system operating at microwave frequencies in the Ku band. Measurements of two fabricated prototypes showcase a large directivity, as predicted with simulations. xml:lang="fr"

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…

Design of Knowledge Bases for Plant Gene Regulatory Networks.

PubMed

Mukundi, Eric; Gomez-Cano, Fabio; Ouma, Wilberforce Zachary; Grotewold, Erich

2017-01-01

Developing a knowledge base that contains all the information necessary for the researcher studying gene regulation in a particular organism can be accomplished in four stages. This begins with defining the data scope. We describe here the necessary information and resources, and outline the methods for obtaining data. The second stage consists of designing the schema, which involves defining the entire arrangement of the database in a systematic plan. The third stage is the implementation, defined by actualization of the database by using software according to a predefined schema. The final stage is development, where the database is made available to users in a web-accessible system. The result is a knowledgebase that integrates all the information pertaining to gene regulation, and which is easily expandable and transferable.

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…

Process Induction: Researching Skills Development across the Social Studies Curriculum. Middle Grades.

ERIC Educational Resources Information Center

Peters, Richard O.

This document discusses the use of process induction and the proactive action model to teach research skills across the social studies curriculum. Process induction is the ability of an individual to transfer schema related knowledge and skills to other situations and settings, to use knowledge and process skills in new and diverse instances to…

Fundamental Research in Engineering Education. Identifying and Repairing Student Misconceptions in Thermal and Transport Science: Concept Inventories and Schema Training Studies

ERIC Educational Resources Information Center

Miller, Ronald L.; Streveler, Ruth A.; Yang, Dazhi; Roman, Aidsa I. Santiago

2011-01-01

This paper summarizes progress on two related lines of chemical engineering education research: 1) identifying persistent student misconceptions in thermal and transport science (fluid mechanics, heat transfer, and thermodynamics); and, 2) developing a method to help students repair these misconceptions. Progress on developing the Thermal and…

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

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

Chroni - an Android Application for Geochronologists to Access Archived Sample Analyses from the NSF-Funded Geochron.Org Data Repository.

NASA Astrophysics Data System (ADS)

Nettles, J. J.; Bowring, J. F.

2014-12-01

NSF requires data management plans as part of funding proposals and geochronologists, among other scientists, are archiving their data and results to the public cloud archives managed by the NSF-funded Integrated Earth Data Applications, or IEDA. GeoChron is a database for geochronology housed within IEDA. The software application U-Pb_Redux developed at the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES.org) at the College of Charleston provides seamless connectivity to GeoChron for uranium-lead (U-Pb) geochronologists to automatically upload and retrieve their data and results. U-Pb_Redux also manages publication-quality documents including report tables and graphs. CHRONI is a lightweight mobile application for Android devices that provides easy access to these archived data and results. With CHRONI, U-Pb geochronologists can view archived data and analyses downloaded from the Geochron database, or any other location, in a customizable format. CHRONI uses the same extensible markup language (XML) schema and documents used by U-Pb_Redux and GeoChron. Report Settings are special XML files that can be customized in U-Pb_Redux, stored in the cloud, and then accessed and used in CHRONI to create the same customized data display on the mobile device. In addition to providing geologists effortless and mobile access to archived data and analyses, CHRONI allows users to manage their GeoChron credentials, quickly download private and public files via a specified IEDA International Geo Sample Number (IGSN) or URL, and view specialized graphics associated with particular IGSNs. Future versions of CHRONI will be developed to support iOS compatible devices. CHRONI is an open source project under the Apache 2 license and is hosted at https://github.com/CIRDLES/CHRONI. We encourage community participation in its continued development.

Migration Stories: Upgrading a PDS Archive to PDS4

NASA Astrophysics Data System (ADS)

Kazden, D. P.; Walker, R. J.; Mafi, J. N.; King, T. A.; Joy, S. P.; Moon, I. S.

2015-12-01

Increasing bandwidth, storage capacity and computational capabilities have greatly increased our ability to access data and use them. A significant challenge, however, is to make data archived under older standards useful in the new data environments. NASA's Planetary Data System (PDS) recently released version 4 of its information model (PDS4). PDS4 is an improvement and has advantages over previous versions. PDS4 adopts the XML standard for metadata and expresses structural requirements with XML Schema and content constraints by using Schematron. This allows for thorough validation by using off the shelf tools. This is a substantial improvement over previous PDS versions. PDS4 was designed to improve discoverability of products (resources) in a PDS archive. These additions allow for more uniform metadata harvesting from the collection level to the product level. New tools and services are being deployed that depend on the data adhering to the PDS4 model. However, the PDS has been an operational archive since 1989 and has large holdings that are compliant with previous versions of the PDS information model. The challenge is the make the older data accessible and useable with the new PDS4 based tools. To provide uniform utility and access to the entire archive the older data must be migrated to the PDS4 model. At the Planetary Plasma Interactions (PPI) Node of the PDS we've been actively planning and preparing to migrate our legacy archive to the new PDS4 standards for several years. With the release of the PDS4 standards we have begun the migration of our archive. In this presentation we will discuss the preparation of the data for the migration and how we are approaching this task. The presentation will consist of a series of stories to describe our experiences and the best practices we have learned.

NASA Tech Briefs, December 2008

NASA Technical Reports Server (NTRS)

2008-01-01

Topics covered include: Crew Activity Analyzer; Distributing Data to Hand-Held Devices in a Wireless Network; Reducing Surface Clutter in Cloud Profiling Radar Data; MODIS Atmospheric Data Handler; Multibeam Altimeter Navigation Update Using Faceted Shape Model; Spaceborne Hybrid-FPGA System for Processing FTIR Data; FPGA Coprocessor for Accelerated Classification of Images; SiC JFET Transistor Circuit Model for Extreme Temperature Range; TDR Using Autocorrelation and Varying-Duration Pulses; Update on Development of SiC Multi-Chip Power Modules; Radio Ranging System for Guidance of Approaching Spacecraft; Electromagnetically Clean Solar Arrays; Improved Short-Circuit Protection for Power Cells in Series; Electromagnetically Clean Solar Arrays; Logic Gates Made of N-Channel JFETs and Epitaxial Resistors; Improved Short-Circuit Protection for Power Cells in Series; Communication Limits Due to Photon-Detector Jitter; System for Removing Pollutants from Incinerator Exhaust; Sealing and External Sterilization of a Sample Container; Converting EOS Data from HDF-EOS to netCDF; HDF-EOS 2 and HDF-EOS 5 Compatibility Library; HDF-EOS Web Server; HDF-EOS 5 Validator; XML DTD and Schemas for HDF-EOS; Converting from XML to HDF-EOS; Simulating Attitudes and Trajectories of Multiple Spacecraft; Specialized Color Function for Display of Signed Data; Delivering Alert Messages to Members of a Work Force; Delivering Images for Mars Rover Science Planning; Oxide Fiber Cathode Materials for Rechargeable Lithium Cells; Electrocatalytic Reduction of Carbon Dioxide to Methane; Heterogeneous Superconducting Low-Noise Sensing Coils; Progress toward Making Epoxy/Carbon-Nanotube Composites; Predicting Properties of Unidirectional-Nanofiber Composites; Deployable Crew Quarters; Nonventing, Regenerable, Lightweight Heat Absorber; Miniature High-Force, Long-Stroke SMA Linear Actuators; "Bootstrap" Configuration for Multistage Pulse-Tube Coolers; Reducing Liquid Loss during Ullage Venting in Microgravity; Ka-Band Transponder for Deep-Space Radio Science; Replication of Space-Shuttle Computers in FPGAs and ASICs; Demisable Reaction-Wheel Assembly; Spatial and Temporal Low-Dimensional Models for Fluid Flow; Advanced Land Imager Assessment System; Range Imaging without Moving Parts.

Introducing ADES: A New IAU Astrometry Data Exchange Standard

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

An Open Source Tool to Test Interoperability

NASA Astrophysics Data System (ADS)

Bermudez, L. E.

2012-12-01

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

Future Concepts for Realtime Data Interfaces for Control Centers

NASA Technical Reports Server (NTRS)

Kearney, Mike W., III

2004-01-01

Existing methods of exchanging realtime data between the major control centers in the International Space Station program have resulted in a patchwork of local formats being imposed on each Mission Control Center. This puts the burden on a data customer to comply with the proprietary data formats of each data supplier. This has increased the cost and complexity for each participant, limited access to mission data and hampered the development of efficient and flexible operations concepts. Ideally, a universal format should be promoted in the industry to prevent the unnecessary burden of each center processing a different data format standard for every external interface with another center. With the broad acceptance of XML and other conventions used in other industries, it is now time for the Aerospace industry to fully engage and establish such a standard. This paper will briefly consider the components that would be required by such a standard (XML schema, data dictionaries, etc.) in order to accomplish the goal of a universal low-cost interface, and acquire broad industry acceptance. We will then examine current approaches being developed by standards bodies and other groups. The current state of CCSDS panel work will be reviewed, with a survey of the degree of industry acceptance. Other widely accepted commercial approaches will be considered, sometimes complimentary to the standards work, but sometimes not. The question is whether de facto industry standards are in concert with, or in conflict with the direction of the standards bodies. And given that state of affairs, the author will consider whether a new program establishing its Mission Control Center should implement a data interface based on those standards. The author proposes that broad industry support to unify the various efforts will enable collaboration between control centers and space programs to a wider degree than is currently available. This will reduce the cost for programs to provide realtime access to their data, hence reducing the cost of access to space, and benefiting the industry as a whole.

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,…

Neurobiology of Schemas and Schema-Mediated Memory.

PubMed

Gilboa, Asaf; Marlatte, Hannah

2017-08-01

Schemas are superordinate knowledge structures that reflect abstracted commonalities across multiple experiences, exerting powerful influences over how events are perceived, interpreted, and remembered. Activated schema templates modulate early perceptual processing, as they get populated with specific informational instances (schema instantiation). Instantiated schemas, in turn, can enhance or distort mnemonic processing from the outset (at encoding), impact offline memory transformation and accelerate neocortical integration. Recent studies demonstrate distinctive neurobiological processes underlying schema-related learning. Interactions between the ventromedial prefrontal cortex (vmPFC), hippocampus, angular gyrus (AG), and unimodal associative cortices support context-relevant schema instantiation and schema mnemonic effects. The vmPFC and hippocampus may compete (as suggested by some models) or synchronize (as suggested by others) to optimize schema-related learning depending on the specific operationalization of schema memory. This highlights the need for more precise definitions of memory schemas. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

PubMed Central

Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-01-01

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists. Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X. Contact: duccio.cavalieri@unifi.it; sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21653523

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

Dynamic publication model for neurophysiology databases.

PubMed

Gardner, D; Abato, M; Knuth, K H; DeBellis, R; Erde, S M

2001-08-29

We have implemented a pair of database projects, one serving cortical electrophysiology and the other invertebrate neurones and recordings. The design for each combines aspects of two proven schemes for information interchange. The journal article metaphor determined the type, scope, organization and quantity of data to comprise each submission. Sequence databases encouraged intuitive tools for data viewing, capture, and direct submission by authors. Neurophysiology required transcending these models with new datatypes. Time-series, histogram and bivariate datatypes, including illustration-like wrappers, were selected by their utility to the community of investigators. As interpretation of neurophysiological recordings depends on context supplied by metadata attributes, searches are via visual interfaces to sets of controlled-vocabulary metadata trees. Neurones, for example, can be specified by metadata describing functional and anatomical characteristics. Permanence is advanced by data model and data formats largely independent of contemporary technology or implementation, including Java and the XML standard. All user tools, including dynamic data viewers that serve as a virtual oscilloscope, are Java-based, free, multiplatform, and distributed by our application servers to any contemporary networked computer. Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support.

LGIST: Learning Generalized Image Schemas for Transfer

DTIC Science & Technology

2008-02-01

and learning methods as developmental psychologists do, as plausible mechanisms for human cognitive development . Why might DARPA care about... cognitive development , and possibly extending to all sensori-motor perceptual modalities [21, 22]. Almost all image-schematic “ theories ” are post-hoc...Warfighter Interface Division NUMBER( S ) Cognitive Systems Branch Wright-Patterson AFB OH 45433-7022 AFRL-RH-WP-TR-2008-0041 12

Effects of the Schema Therapy and Mindfulness on the Maladaptive Schemas Hold by the Psoriasis Patients with the Psychopathology Symptoms

PubMed Central

Gojani, Parvin Jamali; Masjedi, Mohsen; Khaleghipour, Shahnaz; Behzadi, Ehsan

2017-01-01

Background: This study aimed to compare the effects of the schema along with mindfulness-based therapies in the psoriasis patients. Materials and Methods: This semi-experimental study with post- and pre-tests was conducted on the psoriasis patients in the Dermatology Clinic of the Isfahan Alzahra Hospital, Iran using the convenience sampling in 2014. The patients had a low general health score. The experimental groups included two treatment groups of schema-based (n = 8) and mindfulness (n = 8). Both groups received eight 90-min sessions therapy once a week; they were compared with 8 patients in the control group. To evaluate the psoriasis patients’ maladaptive schema, Young schema questionnaire was used. Data were analyzed through the covariance analysis test. Results: There was a significant difference between the schema-based therapy and mindfulness groups with the control group. There was also a significant difference between the schema-based therapy groups consisting of the defeated schema, dependence/incompetence schema, devotion schema, stubbornly criteria schema, merit schema, restraint/inadequate self-discipline schema, and the control group. Moreover, a significant difference existed between the maladaptive schema of mindfulness therapy group and the controls. There was a significant difference concerning the improvement of the psychopathologic symptoms between the mindfulness therapy group and the control group. Conclusions: This study showed similar effects of both the schema and mindfulness-based therapies on the maladaptive schemas in improving the psoriasis patients with the psychopathologic symptoms. PMID:28217649

Frequency-selective design of wireless power transfer systems for controlled access applications

NASA Astrophysics Data System (ADS)

Maschino, Tyler Stephen

Wireless power transfer (WPT) has become a common way to charge or power many types of devices, ranging from cell phones to electric toothbrushes. WPT became popular through the introduction of a transmission mode known as strongly coupled magnetic resonance (SCMR). This means of transmission is non-radiative and enables mid-range WPT. Shortly after the development of WPT via SCMR, a group of researchers introduced the concept of resonant repeaters, which allows power to hop from the source to the device. These repeaters are in resonance with the WPT system, which enables them to propagate the power wirelessly with minimal losses to the environment. Resonant repeaters have rekindled the dream of ubiquitous wireless power. Inherent risks come with the realization of such a dream. One of the most prominent risks, which we set out in this thesis to address, is that of accessibility to the WPT system. We propose the incorporation of a controlled access schema within a WPT system to prevent unwarranted use of wireless power. Our thesis discusses the history of electromagnetism, examines the inception of WPT via SCMR, evaluates recent developments in WPT, and further elaborates on the controlled access schema we wish to contribute to the field.

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…

Hybrid Schema Matching for Deep Web

NASA Astrophysics Data System (ADS)

Chen, Kerui; Zuo, Wanli; He, Fengling; Chen, Yongheng

Schema matching is the process of identifying semantic mappings, or correspondences, between two or more schemas. Schema matching is a first step and critical part of data integration. For schema matching of deep web, most researches only interested in query interface, while rarely pay attention to abundant schema information contained in query result pages. This paper proposed a mixed schema matching technique, which combines attributes that appeared in query structures and query results of different data sources, and mines the matched schemas inside. Experimental results prove the effectiveness of this method for improving the accuracy of schema matching.

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.

Predicting Host Level Reachability via Static Analysis of Routing Protocol Configuration

DTIC Science & Technology

2007-09-01

check_function_bodies = false; SET client_min_messages = warning; -- -- Name: SCHEMA public; Type: COMMENT; Schema: -; Owner: postgres -- COMMENT...public; Owner: mcmanst -- -- -- Name: public; Type: ACL; Schema: -; Owner: postgres -- REVOKE ALL ON SCHEMA public FROM PUBLIC; REVOKE...ALL ON SCHEMA public FROM postgres ; GRANT ALL ON SCHEMA public TO postgres ; GRANT ALL ON SCHEMA public TO PUBLIC; -- -- PostgreSQL database

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).

The evolution of the CUAHSI Water Markup Language (WaterML)

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Valentine, D.; Maidment, D.; Tarboton, D. G.; Whiteaker, T.; Hooper, R.; Kirschtel, D.; Rodriguez, M.

2009-04-01

The CUAHSI Hydrologic Information System (HIS, his.cuahsi.org) uses web services as the core data exchange mechanism which provides programmatic connection between many heterogeneous sources of hydrologic data and a variety of online and desktop client applications. The service message schema follows the CUAHSI Water Markup Language (WaterML) 1.x specification (see OGC Discussion Paper 07-041r1). Data sources that can be queried via WaterML-compliant water data services include national and international repositories such as USGS NWIS (National Water Information System), USEPA STORET (Storage & Retrieval), USDA SNOTEL (Snowpack Telemetry), NCDC ISH and ISD(Integrated Surface Hourly and Daily Data), MODIS (Moderate Resolution Imaging Spectroradiometer), and DAYMET (Daily Surface Weather Data and Climatological Summaries). Besides government data sources, CUAHSI HIS provides access to a growing number of academic hydrologic observation networks. These networks are registered by researchers associated with 11 hydrologic observatory testbeds around the US, and other research, government and commercial groups wishing to join the emerging CUAHSI Water Data Federation. The Hydrologic Information Server (HIS Server) software stack deployed at NSF-supported hydrologic observatory sites and other universities around the country, supports a hydrologic data publication workflow which includes the following steps: (1) observational data are loaded from static files or streamed from sensors into a local instance of an Observations Data Model (ODM) database; (2) a generic web service template is configured for the new ODM instance to expose the data as a WaterML-compliant water data service, and (3) the new water data service is registered at the HISCentral registry (hiscentral.cuahsi.org), its metadata are harvested and semantically tagged using concepts from a hydrologic ontology. As a result, the new service is indexed in the CUAHSI central metadata catalog, and becomes available for spatial and semantics-based queries. The main component of interoperability across hydrologic data repositories in CUAHSI HIS is mapping different repository schemas and semantics to a shared community information model for observations made at stationary points. This information model has been implemented as both a relational schema (ODM) and an XML schema (WaterML). Its main design drivers have been data storage and data interchange needs of hydrology researchers, a series of community reviews of the ODM, and the practices of hydrologic data modeling and presentation adopted by federal agencies as observed in agency online data access applications, such as NWISWeb and USEPA STORET. The goal of the first version of WaterML was to encode the semantics of hydrologic observations discovery and retrieval and implement water data services in a way that is generic across different data providers. In particular, this implied maintaining a single common representation for the key constructs returned to web service calls, related to observations, features of interest, observation procedures, observation series, etc. Another WaterML design consideration was to create (in version 1 of CUAHSI HIS in particular) a fairly rigid, compact, and simple XML schema which was easy to generate and parse, thus creating the least barrier for adoption by hydrologists. Each of the three main request methods in the water data web services - GetSiteInfo, GetVariableInfo, and GetValues - has a corresponding response element in WaterML: SiteResponse, VariableResponse, and TimeSeriesResponse. The strictness and compactness of the first version of WaterML supported its community adoption. Over the last two years, several ODM and WaterML implementations for various platforms have emerged, and several Water Data Services client applications have been created by outside groups in both industry and academia. In a significant development, the WaterML specification has been adopted by federal agencies. The experimental USGS NWIS Daily Values web service returns WaterML-compliant TimeSeriesResponse. NCDC is also prototyping WaterML for data delivery, and has developed a REST-based service that generates WaterML- compliant output for its integrated station network. These agency-supported web services provide a much more efficient way to deliver agency data compared to the web site scraper services that the CUAHSI HIS project developed initially. Adoption of WaterML by the US Geological Survey is particularly significant because the USGS maintains by far the largest water data repository in the United States. For version 1.1, WaterML has evolved to reflect the deployment experience at hydrologic observatory testbeds, as well as feedback from hydrologic data repository managers at federal and state agencies. Further development of WaterML and enhancement of the underlying information model is the focus of the recently established OGC Hydrology Domain Working Group, whose mission is to profile OGC standards (GML, O&M, SOS, WCS, WFS) for the water resources domain and thus ensure WaterML's wider applicability and easier implementation. WaterML 2.0 is envisioned as an OGC-compliant application schema that supports OGC features, can express different types of observations and various groupings of observations, and allows researchers to define custom metadata elements. This presentation will discuss the information model underlying WaterML and describe the rationale, design drivers and evolution of WaterML and the water data services, illustrating their recent application in the context of CUAHSI HIS and the hydrologic observatory testbeds.

Performance of the High Sensitivity Open Source Multi-GNSS Assisted GNSS Reference Server.

NASA Astrophysics Data System (ADS)

Sarwar, Ali; Rizos, Chris; Glennon, Eamonn

2015-06-01

The Open Source GNSS Reference Server (OSGRS) exploits the GNSS Reference Interface Protocol (GRIP) to provide assistance data to GPS receivers. Assistance can be in terms of signal acquisition and in the processing of the measurement data. The data transfer protocol is based on Extensible Mark-up Language (XML) schema. The first version of the OSGRS required a direct hardware connection to a GPS device to acquire the data necessary to generate the appropriate assistance. Scenarios of interest for the OSGRS users are weak signal strength indoors, obstructed outdoors or heavy multipath environments. This paper describes an improved version of OSGRS that provides alternative assistance support from a number of Global Navigation Satellite Systems (GNSS). The underlying protocol to transfer GNSS assistance data from global casters is the Networked Transport of RTCM (Radio Technical Commission for Maritime Services) over Internet Protocol (NTRIP), and/or the RINEX (Receiver Independent Exchange) format. This expands the assistance and support model of the OSGRS to globally available GNSS data servers connected via internet casters. A variety of formats and versions of RINEX and RTCM streams become available, which strengthens the assistance provisioning capability of the OSGRS platform. The prime motivation for this work was to enhance the system architecture of the OSGRS to take advantage of globally available GNSS data sources. Open source software architectures and assistance models provide acquisition and data processing assistance for GNSS receivers operating in weak signal environments. This paper describes test scenarios to benchmark the OSGRSv2 performance against other Assisted-GNSS solutions. Benchmarking devices include the SPOT satellite messenger, MS-Based & MS-Assisted GNSS, HSGNSS (SiRFstar-III) and Wireless Sensor Networks Assisted-GNSS. Benchmarked parameters include the number of tracked satellites, the Time to Fix First (TTFF), navigation availability and accuracy. Three different configurations of Multi-GNSS assistance servers were used, namely Cloud-Client-Server, the Demilitarized Zone (DMZ) Client-Server and PC-Client-Server; with respect to the connectivity location of client and server. The impact on the performance based on server and/or client initiation, hardware capability, network latency, processing delay and computation times with their storage, scalability, processing and load sharing capabilities, were analysed. The performance of the OSGRS is compared against commercial GNSS, Assisted-GNSS and WSN-enabled GNSS devices. The OSGRS system demonstrated lower TTFF and higher availability.

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.

Sea Level Station Metadata for Tsunami Detection, Warning and Research

NASA Astrophysics Data System (ADS)

Stroker, K. J.; Marra, J.; Kari, U. S.; Weinstein, S. A.; Kong, L.

2007-12-01

The devastating earthquake and tsunami of December 26, 2004 has greatly increased recognition of the need for water level data both from the coasts and the deep-ocean. In 2006, the National Oceanic and Atmospheric Administration (NOAA) completed a Tsunami Data Management Report describing the management of data required to minimize the impact of tsunamis in the United States. One of the major gaps defined in this report is the access to global coastal water level data. NOAA's National Geophysical Data Center (NGDC) and National Climatic Data Center (NCDC) are working cooperatively to bridge this gap. NOAA relies on a network of global data, acquired and processed in real-time to support tsunami detection and warning, as well as high-quality global databases of archived data to support research and advanced scientific modeling. In 2005, parties interested in enhancing the access and use of sea level station data united under the NOAA NCDC's Integrated Data and Environmental Applications (IDEA) Center's Pacific Region Integrated Data Enterprise (PRIDE) program to develop a distributed metadata system describing sea level stations (Kari et. al., 2006; Marra et.al., in press). This effort started with pilot activities in a regional framework and is targeted at tsunami detection and warning systems being developed by various agencies. It includes development of the components of a prototype sea level station metadata web service and accompanying Google Earth-based client application, which use an XML-based schema to expose, at a minimum, information in the NOAA National Weather Service (NWS) Pacific Tsunami Warning Center (PTWC) station database needed to use the PTWC's Tide Tool application. As identified in the Tsunami Data Management Report, the need also exists for long-term retention of the sea level station data. NOAA envisions that the retrospective water level data and metadata will also be available through web services, using an XML-based schema. Five high-priority metadata requirements identified at a water level workshop held at the XXIV IUGG Meeting in Perugia will be addressed: consistent, validated, and well defined numbers (e.g. amplitude); exact location of sea level stations; a complete record of sea level data stored in the archive; identifying high-priority sea level stations; and consistent definitions. NOAA's National Geophysical Data Center (NGDC) and co-located World Data Center for Solid Earth Geophysics (including tsunamis) would hold the archive of the sea level station data and distribute the standard metadata. Currently, NGDC is also archiving and distributing the DART buoy deep-ocean water level data and metadata in standards based formats. Kari, Uday S., John J. Marra, Stuart A. Weinstein, 2006 A Tsunami Focused Data Sharing Framework For Integration of Databases that Describe Water Level Station Specifications. AGU Fall Meeting, 2006. San Francisco, California. Marra, John, J., Uday S. Kari, and Stuart A. Weinstein (in press). A Tsunami Detection and Warning-focused Sea Level Station Metadata Web Service. IUGG XXIV, July 2-13, 2007. Perugia, Italy.

Psychometric Properties and Normative values of Early Maladaptive Schema Questionnaires Set for Children and Adolescents (SQS).

PubMed

Güner, Olcay

2017-03-01

The Early Maladaptive Schema Questionnaires Set for Children and Adolescents (SQS) was developed to assess early maladaptive schemas in children between the ages of 10 and 16 in Turkey. The SQS consists of five questionnaires that represent five schema domains in Young's schema theory. Psychometric properties (n = 983) and normative values (n = 2250) of SQS were investigated in children and adolescents between the ages of 10 and 16. Both exploratory and confirmatory factor analyses were performed. Results revealed 15 schema factors under five schema domains, with good fit indexes. A total of 14 schema factors were in line with Young's early maladaptive schemas. In addition to these factors, one new schema emerged: self-disapproval. Reliability analyses showed that SQS has high internal consistency and consistency over a 1-month interval. Correlations of SQS with the Adjective Check List (ACL), the Inventory of Parent and Peer Attachment (IPPA), the Symptom Assessment (SA-45) and the Young Schema Questionnaire (YSQ) were investigated to assess criterion validity, and the correlations revealed encouraging results. SQS significantly differentiated between children who have clinical diagnoses (n = 78) and children who have no diagnosis (n = 100). Finally, general normative values (n = 2,250) were determined for age groups, gender and age/gender groups. In conclusion, the early maladaptive schema questionnaires set for children and adolescents turned out to be a reliable and valid questionnaire with standard scores.Copyright © 2016 John Wiley & Sons, Ltd. The early maladaptive schema questionnaires set for children and adolescents (SQS) is a psychometrically reliable and valid measure of early maladaptive schemas for children between the ages of 10 and 16. SQS consists of five schema domains that represent Young's schema domains including 15 early maladaptive schemas and 97 items. Normative values for each schema were determined for age, gender and age/gender groups. Clinically, SQS presents valuable information about early maladaptive schemas during childhood and adolescence, before such schemas become more pervasive and persistent. Copyright © 2016 John Wiley & Sons, Ltd.

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.

A narrative review of schemas and schema therapy outcomes in the eating disorders.

PubMed

Pugh, Matthew

2015-07-01

Whilst cognitive-behavioural therapy has demonstrated efficacy in the treatment of eating disorders, therapy outcomes and current conceptualizations still remain inadequate. In light of these shortcomings there has been growing interest in the utility of schema therapy applied to eating pathology. The present article first provides a narrative review of empirical literature exploring schemas and schema processes in eating disorders. Secondly, it critically evaluates outcome studies assessing schema therapy applied to eating disorders. Current evidence lends support to schema-focused conceptualizations of eating pathology and confirms that eating disorders are characterised by pronounced maladaptive schemas. Treatment outcomes also indicate that schema therapy, the schema-mode approach, and associated techniques are promising interventions for complex eating disorders. Implications for clinical practice and future directions for research are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Mental Schemas Hamper Memory Storage of Goal-Irrelevant Information

PubMed Central

Sweegers, C. C. G.; Coleman, G. A.; van Poppel, E. A. M.; Cox, R.; Talamini, L. M.

2015-01-01

Mental schemas exert top-down control on information processing, for instance by facilitating the storage of schema-related information. However, given capacity-limits and competition in neural network processing, schemas may additionally exert their effects by suppressing information with low momentary relevance. In particular, when existing schemas suffice to guide goal-directed behavior, this may actually reduce encoding of the redundant sensory input, in favor of gaining efficiency in task performance. The present experiment set out to test this schema-induced shallow encoding hypothesis. Our approach involved a memory task in which faces had to be coupled to homes. For half of the faces the responses could be guided by a pre-learned schema, for the other half of the faces such a schema was not available. Memory storage was compared between schema-congruent and schema-incongruent items. To characterize putative schema effects, memory was assessed both with regard to visual details and contextual aspects of each item. The depth of encoding was also assessed through an objective neural measure: the parietal old/new ERP effect. This ERP effect, observed between 500–800 ms post-stimulus onset, is thought to reflect the extent of recollection: the retrieval of a vivid memory, including various contextual details from the learning episode. We found that schema-congruency induced substantial impairments in item memory and even larger ones in context memory. Furthermore, the parietal old/new ERP effect indicated higher recollection for the schema-incongruent than the schema-congruent memories. The combined findings indicate that, when goals can be achieved using existing schemas, this can hinder the in-depth processing of novel input, impairing the formation of perceptually detailed and contextually rich memory traces. Taking into account both current and previous findings, we suggest that schemas can both positively and negatively bias the processing of sensory input. An important determinant in this matter is likely related to momentary goals, such that mental schemas facilitate memory processing of goal-relevant input, but suppress processing of goal-irrelevant information. Highlights – Schema-congruent information suffers from shallow encoding. – Schema congruency induces poor item and context memory. – The parietal old/new effect is less pronounced for schema-congruent items. – Schemas exert different influences on memory formation depending on current goals. PMID:26635582

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.

The role of aggression-related early maladaptive schemas and schema modes in aggression in a prisoner sample.

PubMed

Dunne, Ashley L; Gilbert, Flora; Lee, Stuart; Daffern, Michael

2018-05-01

Contemporary social-cognitive aggression theory and extant empirical research highlights the relationship between certain Early Maladaptive Schemas (EMSs) and aggression in offenders. To date, the related construct of schema modes, which presents a comprehensive and integrated schema unit, has received scant empirical attention. Furthermore, EMSs and schema modes have yet to be examined concurrently with respect to aggressive behavior. This study examined associations between EMSs, schema modes, and aggression in an offender sample. Two hundred and eight adult male prisoners completed self-report psychological tests measuring their histories of aggression, EMSs, and schema modes. Regression analyses revealed that EMSs were significantly associated with aggression but did not account for a unique portion of variance once the effects of schema modes were taken into account. Three schema modes, Enraged Child, Impulsive Child, and Bully and Attack, significantly predicted aggression. These findings support the proposition that schema modes characterized by escalating states of anger, rage, and impulsivity characterize aggressive offenders. In this regard, we call attention to the need to include schema modes in contemporary social-cognitive aggression theories, and suggest that systematic assessment and treatment of schema modes has the potential to enhance outcomes with violent offenders. © 2018 Wiley Periodicals, Inc.

Solving Word Problems using Schemas: A Review of the Literature

PubMed Central

Powell, Sarah R.

2011-01-01

Solving word problems is a difficult task for students at-risk for or with learning disabilities (LD). One instructional approach that has emerged as a valid method for helping students at-risk for or with LD to become more proficient at word-problem solving is using schemas. A schema is a framework for solving a problem. With a schema, students are taught to recognize problems as falling within word-problem types and to apply a problem solution method that matches that problem type. This review highlights two schema approaches for 2nd- and 3rd-grade students at-risk for or with LD: schema-based instruction and schema-broadening instruction. A total of 12 schema studies were reviewed and synthesized. Both types of schema approaches enhanced the word-problem skill of students at-risk for or with LD. Based on the review, suggestions are provided for incorporating word-problem instruction using schemas. PMID:21643477

Systematic plan of building Web geographic information system based on ActiveX control

NASA Astrophysics Data System (ADS)

Zhang, Xia; Li, Deren; Zhu, Xinyan; Chen, Nengcheng

2003-03-01

A systematic plan of building Web Geographic Information System (WebGIS) using ActiveX technology is proposed in this paper. In the proposed plan, ActiveX control technology is adopted in building client-side application, and two different schemas are introduced to implement communication between controls in users¡ browser and middle application server. One is based on Distribute Component Object Model (DCOM), the other is based on socket. In the former schema, middle service application is developed as a DCOM object that communicates with ActiveX control through Object Remote Procedure Call (ORPC) and accesses data in GIS Data Server through Open Database Connectivity (ODBC). In the latter, middle service application is developed using Java language. It communicates with ActiveX control through socket based on TCP/IP and accesses data in GIS Data Server through Java Database Connectivity (JDBC). The first one is usually developed using C/C++, and it is difficult to develop and deploy. The second one is relatively easy to develop, but its performance of data transfer relies on Web bandwidth. A sample application is developed using the latter schema. It is proved that the performance of the sample application is better than that of some other WebGIS applications in some degree.

Astronomical Data Integration Beyond the Virtual Observatory

NASA Astrophysics Data System (ADS)

Lemson, G.; Laurino, O.

2015-09-01

"Data integration" generally refers to the process of combining data from different source data bases into a unified view. Much work has been devoted in this area by the International Virtual Observatory Alliance (IVOA), allowing users to discover and access databases through standard protocols. However, different archives present their data through their own schemas and users must still select, filter, and combine data for each archive individually. An important reason for this is that the creation of common data models that satisfy all sub-disciplines is fraught with difficulties. Furthermore it requires a substantial amount of work for data providers to present their data according to some standard representation. We will argue that existing standards allow us to build a data integration framework that works around these problems. The particular framework requires the implementation of the IVOA Table Access Protocol (TAP) only. It uses the newly developed VO data modelling language (VO-DML) specification, which allows one to define extensible object-oriented data models using a subset of UML concepts through a simple XML serialization language. A rich mapping language allows one to describe how instances of VO-DML data models are represented by the TAP service, bridging the possible mismatch between a local archive's schema and some agreed-upon representation of the astronomical domain. In this so called local-as-view approach to data integration, “mediators" use the mapping prescriptions to translate queries phrased in terms of the common schema to the underlying TAP service. This mapping language has a graphical representation, which we expose through a web based graphical “drag-and-drop-and-connect" interface. This service allows any user to map the holdings of any TAP service to the data model(s) of choice. The mappings are defined and stored outside of the data sources themselves, which allows the interface to be used in a kind of crowd-sourcing effort to annotate any remote database of interest. This reduces the burden of publishing one's data and allows a great flexibility in the definition of the views through which particular communities might wish to access remote archives. At the same time, the framework easies the user's effort to select, filter, and combine data from many different archives, so as to build knowledge bases for their analysis. We will present the framework and demonstrate a prototype implementation. We will discuss ideas for producing the missing elements, in particular the query language and the implementation of mediator tools to translate object queries to ADQL

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

Parsing GML data based on integrative GML syntactic and semantic schemas database

NASA Astrophysics Data System (ADS)

Miao, Lizhi; Zhang, Shuliang; Lu, Guonian; Gao, Xiaoli; Jiao, Donglai; Gan, Jiayan

2007-06-01

This paper proposes a new method to parse various application schemas of Geography Markup Language (GML) for understanding syntax and semantic of their element and type in order to implement uniform interpretation of the same GML instance data among diverse users. The proposed method generates an Integrative GML Syntactic and Semantic Schemas Database (IGSSSDB) from GML3.1 core schemas and corresponding application schema. This paper parses GML data based on IGSSSDB, which is composed of syntactic and semantic information, nesting information and mapping rules of GML core schemas and application schemas. Three kinds of relational tables are designed for storing information from schemas when constructing IGSSSDB. Those are info tables for schemas included and namespace imported in application schemas, tables for information related to schemas and catalog tables of core schemas. In relational tables, we propose to use homologous regular expression to describe model of elements and complex types in schemas, which can ensure model complete and readable. Based on IGSSSDB, we design and develop many APIs to implement GML data parsing, and can process syntactic and semantic information of GML data from diverse fields and users. At the latter part of this paper, test study is implemented to show that the proposed method is feasible and appropriate for parsing GML data. Also, it founds a good basis for future GML data studies such as storage, index and query etc.

A comparison of database systems for XML-type data.

PubMed

Risse, Judith E; Leunissen, Jack A M

2010-01-01

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

XML Flight/Ground Data Dictionary Management

NASA Technical Reports Server (NTRS)

Wright, Jesse; Wiklow, Colette

2007-01-01

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

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.

Comparison of early maladaptive schemas and parenting origins in patients with opioid abuse and non-abusers.

PubMed

Jalali, Mohammad Reza; Zargar, Mohammad; Salavati, Mojgan; Kakavand, Ali Reza

2011-01-01

The aim of this study was to examine the difference of early maladaptive schemas and parenting origins in opioid abusers and non-opioid abusers. The early maladaptive schemas and parenting origins were compared in 56 opioid abusers and 56 non-opioids abusers. Schemas were assessed by the Young Schema Questionnaire 3rd (short form); and parenting origins were assessed by the Young Parenting Inventory. Data were analyzed by multivariate analysis of variance (MANOVA). The analysis showed that the means for schemas between opioid abusers and non-opioid abusers were different. Chi square test showed that parenting origins were significantly associated with their related schemas. The early maladaptive schemas and parenting origins in opioid abusers were more than non-opioid abusers; and parenting origins were related to their Corresponding schemas.

"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…

Early maladaptive schemas in adult patients with attention deficit hyperactivity disorder.

PubMed

Philipsen, Alexandra; Lam, Alexandra P; Breit, Sigrid; Lücke, Caroline; Müller, Helge H; Matthies, Swantje

2017-06-01

The main purpose of this study was to examine whether adult patients with attention deficit hyperactivity disorder (ADHD) demonstrate sets of dysfunctional cognitive beliefs and behavioural tendencies according to Jeffrey Young's schema-focused therapy model. Sets of dysfunctional beliefs (maladaptive schemas) were assessed with the Young Schema Questionnaire (YSQ-S2) in 78 adult ADHD patients and 80 control subjects. Patients with ADHD scored significantly higher than the control group on almost all maladaptive schemas. The 'Failure', 'Defectiveness/Shame', 'Subjugation' and 'Emotional Deprivation' schemas were most pronounced in adult ADHD patients, while only 'Vulnerability to Harm or Illness' did not differ between the two groups. The schemas which were most pronounced in adult patients with ADHD correspond well with their learning histories and core symptoms. By demonstrating the existence of early maladaptive schemas in adults suffering from ADHD, this study suggests that schema theory may usefully be applied to adult ADHD therapy.

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.

Schema representation in patients with ventromedial PFC lesions.

PubMed

Ghosh, Vanessa E; Moscovitch, Morris; Melo Colella, Brenda; Gilboa, Asaf

2014-09-03

Human neuroimaging and animal studies have recently implicated the ventromedial prefrontal cortex (vmPFC) in memory schema, particularly in facilitating new encoding by existing schemas. In humans, the most conspicuous memory disorder following vmPFC damage is confabulation; strategic retrieval models suggest that aberrant schema activation or reinstatement plays a role in confabulation. This raises the possibility that beyond its role in schema-supported memory encoding, the vmPFC is also implicated in schema reinstatement itself. If that is the case, vmPFC lesions should lead to impaired schema-based operations, even on tasks that do not involve memory acquisition. To test this prediction, ten patients with vmPFC damage, four with present or prior confabulation, and a group of twelve matched healthy controls made speeded yes/no decisions as to whether words were closely related to a schema (a visit to the doctor). Ten minutes later, they repeated the task for a new schema (going to bed) with some words related to the first schema included as lures. Last, they rated the degree to which stimuli were related to the second schema. All four vmPFC patients with present or prior confabulation were impaired in rejecting lures and in classifying stimulus belongingness to the schema, even when they were not lures. Nonconfabulating patients performed comparably to healthy adults with high accuracy, comparable reaction times, and similar ratings. These results show for the first time that damage to the human vmPFC, when associated with confabulation, leads to deficient schema reinstatement, which is likely a prerequisite for schema-mediated memory integration. Copyright © 2014 the authors 0270-6474/14/3412057-14$15.00/0.

A Novel Navigation Paradigm for XML Repositories.

ERIC Educational Resources Information Center

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

2002-01-01

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

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.…

SchemaOnRead: A Package for Schema-on-Read in R

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

North, Michael J.

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info,more » Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.« less

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

NASA Technical Reports Server (NTRS)

Hildreth, Bruce L.; Jackson, E. Bruce

2009-01-01

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

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: A Publisher's Perspective.

ERIC Educational Resources Information Center

Andrews, Timothy M.

1999-01-01

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

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

PubMed

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

2010-04-01

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

The Cadmio XML healthcare record.

PubMed

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

2002-01-01

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

Stress affects the neural ensemble for integrating new information and prior knowledge.

PubMed

Vogel, Susanne; Kluen, Lisa Marieke; Fernández, Guillén; Schwabe, Lars

2018-06-01

Prior knowledge, represented as a schema, facilitates memory encoding. This schema-related learning is assumed to rely on the medial prefrontal cortex (mPFC) that rapidly integrates new information into the schema, whereas schema-incongruent or novel information is encoded by the hippocampus. Stress is a powerful modulator of prefrontal and hippocampal functioning and first studies suggest a stress-induced deficit of schema-related learning. However, the underlying neural mechanism is currently unknown. To investigate the neural basis of a stress-induced schema-related learning impairment, participants first acquired a schema. One day later, they underwent a stress induction or a control procedure before learning schema-related and novel information in the MRI scanner. In line with previous studies, learning schema-related compared to novel information activated the mPFC, angular gyrus, and precuneus. Stress, however, affected the neural ensemble activated during learning. Whereas the control group distinguished between sets of brain regions for related and novel information, stressed individuals engaged the hippocampus even when a relevant schema was present. Additionally, stressed participants displayed aberrant functional connectivity between brain regions involved in schema processing when encoding novel information. The failure to segregate functional connectivity patterns depending on the presence of prior knowledge was linked to impaired performance after stress. Our results show that stress affects the neural ensemble underlying the efficient use of schemas during learning. These findings may have relevant implications for clinical and educational settings. Copyright © 2018 Elsevier Inc. All rights reserved.

Occupant behavior models: A critical review of implementation and representation approaches in building performance simulation programs

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

Hong, Tianzhen; Chen, Yixing; Belafi, Zsofia

Occupant behavior (OB) in buildings is a leading factor influencing energy use in buildings. Quantifying this influence requires the integration of OB models with building performance simulation (BPS). This study reviews approaches to representing and implementing OB models in today’s popular BPS programs, and discusses weaknesses and strengths of these approaches and key issues in integrating of OB models with BPS programs. Two of the key findings are: (1) a common data model is needed to standardize the representation of OB models, enabling their flexibility and exchange among BPS programs and user applications; the data model can be implemented usingmore » a standard syntax (e.g., in the form of XML schema), and (2) a modular software implementation of OB models, such as functional mock-up units for co-simulation, adopting the common data model, has advantages in providing a robust and interoperable integration with multiple BPS programs. Such common OB model representation and implementation approaches help standardize the input structures of OB models, enable collaborative development of a shared library of OB models, and allow for rapid and widespread integration of OB models with BPS programs to improve the simulation of occupant behavior and quantification of their impact on building performance.« less

Capturing cooperative interactions with the PSI-MI format

PubMed Central

Van Roey, Kim; Orchard, Sandra; Kerrien, Samuel; Dumousseau, Marine; Ricard-Blum, Sylvie; Hermjakob, Henning; Gibson, Toby J.

2013-01-01

The complex biological processes that control cellular function are mediated by intricate networks of molecular interactions. Accumulating evidence indicates that these interactions are often interdependent, thus acting cooperatively. Cooperative interactions are prevalent in and indispensible for reliable and robust control of cell regulation, as they underlie the conditional decision-making capability of large regulatory complexes. Despite an increased focus on experimental elucidation of the molecular details of cooperative binding events, as evidenced by their growing occurrence in literature, they are currently lacking from the main bioinformatics resources. One of the contributing factors to this deficiency is the lack of a computer-readable standard representation and exchange format for cooperative interaction data. To tackle this shortcoming, we added functionality to the widely used PSI-MI interchange format for molecular interaction data by defining new controlled vocabulary terms that allow annotation of different aspects of cooperativity without making structural changes to the underlying XML schema. As a result, we are able to capture cooperative interaction data in a structured format that is backward compatible with PSI-MI–based data and applications. This will facilitate the storage, exchange and analysis of cooperative interaction data, which in turn will advance experimental research on this fundamental principle in biology. Database URL: http://psi-mi-cooperativeinteractions.embl.de/ PMID:24067240

Occupant behavior models: A critical review of implementation and representation approaches in building performance simulation programs

DOE PAGES

Hong, Tianzhen; Chen, Yixing; Belafi, Zsofia; ...

2017-07-27

Occupant behavior (OB) in buildings is a leading factor influencing energy use in buildings. Quantifying this influence requires the integration of OB models with building performance simulation (BPS). This study reviews approaches to representing and implementing OB models in today’s popular BPS programs, and discusses weaknesses and strengths of these approaches and key issues in integrating of OB models with BPS programs. Two of the key findings are: (1) a common data model is needed to standardize the representation of OB models, enabling their flexibility and exchange among BPS programs and user applications; the data model can be implemented usingmore » a standard syntax (e.g., in the form of XML schema), and (2) a modular software implementation of OB models, such as functional mock-up units for co-simulation, adopting the common data model, has advantages in providing a robust and interoperable integration with multiple BPS programs. Such common OB model representation and implementation approaches help standardize the input structures of OB models, enable collaborative development of a shared library of OB models, and allow for rapid and widespread integration of OB models with BPS programs to improve the simulation of occupant behavior and quantification of their impact on building performance.« less

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.

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

Marketing responsible drinking behavior: comparing the effectiveness of responsible drinking messages tailored to three possible "personality" conceptualizations.

PubMed

York, Valerie K; Brannon, Laura A; Miller, Megan M

2012-01-01

We investigated whether a thoroughly personalized message (tailored to a person's "Big Five" personality traits) or a message matched to an alternate form of self-schema (ideal self-schema) would be more influential than a self-schema matched message (that has been found to be effective) at marketing responsible drinking. We expected the more thoroughly personalized Big Five matched message to be more effective than the self-schema matched message. However, neither the Big Five message nor the ideal self-schema message was more effective than the actual self-schema message. Therefore, research examining self-schema matching should be pursued rather than more complex Big Five matching.

Constraints on Access: Costs and Benefits (Spontaneous Memory for Relevant Experiences)

DTIC Science & Technology

1989-05-01

F. I. M. Craik (Eds.), Levels of processing and human memory. Hillsdale, NJ: Erlbaum. Dewey, J. (1963). How we think. Portions published in R. M...transfer. Pictures (vs. words) and levels of processing and elaborative encoding manipulations are shown to affect directed access but are found to have...includes most 5 6 list-learning experiments, research on schema/script abstraction, and studies of remembering which might manipulate levels of processing

How the Media Effects Schema and the Persuasion Ethics Schema Affect Audience Responses to Antismoking Campaign Messages.

PubMed

Paek, Hye-Jin; Hove, Thomas

2018-05-01

This study examines the roles that the media effects and persuasion ethics schemas play in people's responses to an antismoking ad in South Korea. An online experiment was conducted with 347 adults. The media effects schema was manipulated with news stories on an antismoking campaign's effectiveness, while the persuasion ethics schema was measured and median-split. Analysis of Variance (ANOVA) tests were performed for issue attitudes (Iatt), attitude toward the ad (Aad), and behavioral intention (BI). Results show significant main effects of the media effects schema on the three dependent variables. People in the weak media effects condition had significantly lower Iatt, Aad, and BI than those in either the strong media effects condition or the control condition. This pattern was more pronounced among smokers. While there was no significant main effect of the persuasion ethics schema on any of the dependent variables, a significant interaction effect for persuasion ethics schema and smoking status was found on behavioral intention (BI). Nonsmokers' BI was significantly higher than smokers' in the low-persuasion ethics schema condition, but it was not significant in the high-persuasion ethics schema condition.

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

Schema building profiles among elementary school students in solving problems related to operations of addition to fractions on the basis of mathematic abilities

NASA Astrophysics Data System (ADS)

Gembong, S.; Suwarsono, S. T.; Prabowo

2018-03-01

Schema in the current study refers to a set of action, process, object and other schemas already possessed to build an individual’s ways of thinking to solve a given problem. The current study aims to investigate the schemas built among elementary school students in solving problems related to operations of addition to fractions. The analyses of the schema building were done qualitatively on the basis of the analytical framework of the APOS theory (Action, Process, Object, and Schema). Findings show that the schemas built on students of high and middle ability indicate the following. In the action stage, students were able to add two fractions by way of drawing a picture or procedural way. In the Stage of process, they could add two and three fractions. In the stage of object, they could explain the steps of adding two fractions and change a fraction into addition of fractions. In the last stage, schema, they could add fractions by relating them to another schema they have possessed i.e. the least common multiple. Those of high and middle mathematic abilities showed that their schema building in solving problems related to operations odd addition to fractions worked in line with the framework of the APOS theory. Those of low mathematic ability, however, showed that their schema on each stage did not work properly.

The role of childhood trauma, early maladaptive schemas, emotional schemas and experimental avoidance on depression: A structural equation modeling.

PubMed

Rezaei, Mehdi; Ghazanfari, Firoozeh; Rezaee, Fatemeh

2016-12-30

The present investigation was designed to examine disconnection and rejection (DR) schemas, negative emotional schemas (NESs) and experimental avoidance (EA) as mediating variables of the relationship between the childhood trauma (CT) and depression. Specifically we examined the mediating role of NESs and EA between DR schemas and depression. The study sample consist of 439 female college students (M age =22.47; SD=6.0), of whom 88 met the criteria for current major depressive disorder (MDD) and 351 who had history of MDD in the last 12 months. Subjects were assessed by Structured Clinical Interview for DSM-IV (SCID) and completed the Childhood Trauma Questionnaire (CTQ), the Early Maladaptive Schemas Questionnaire (SQ-SF), the Leahy Emotional Schemas Scale (LESS), the Acceptance and Action Questionnaire (AAQ-II), and the Beck Depression Inventory-II (BDI-II). The findings showed that DR schemas were mediator of the relationship CT and depression but CT through the NESs and EA did not predict depression. NESs were mediator of the relationship between DR schemas and depression and EA was mediator of the relationship between DR schemas and depression. In general, results suggest that intervention of depressed women may need to target the changing of DR schemas, NESs and reduction of EA. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A schema theory analysis of students' think aloud protocols in an STS biology context

NASA Astrophysics Data System (ADS)

Quinlan, Catherine Louise

This dissertation study is a conglomerate of the fields of Science Education and Applied Cognitive Psychology. The goal of this study is to determine what organizational features and knowledge representation patterns high school students exhibit over time for issues pertinent to science and society. Participants are thirteen tenth grade students in a diverse suburban-urban classroom in a northeastern state. Students' think alouds are recorded, pre-, post-, and late-post treatment. Treatment consists of instruction in three Science, Technology, and Society (STS) biology issues, namely the human genome project, nutrition and health, and stem cell research. Coding and analyses are performed using Marshall's knowledge representations---identification knowledge, elaboration knowledge, planning knowledge, and execution knowledge, as well as qualitative research analysis methods. Schema theory, information processing theory, and other applied cognitive theory provide a framework in which to understand and explain students' schema descriptions and progressions over time. The results show that students display five organizational features in their identification and elaboration knowledge. Students also fall into one of four categories according to if they display prior schema or no prior schema, and their orientation "for" or "against," some of the issues. Students with prior schema and orientation "against" display the most robust schema descriptions and schema progressions. Those with no prior schemas and orientation "against" show very modest schema progressions best characterized by their keyword searches. This study shows the importance in considering not only students' integrated schemas but also their individual schemes. A role for the use of a more schema-based instruction that scaffolds student learning is implicated.

Positive clinical psychology and Schema Therapy (ST): The development of the Young Positive Schema Questionnaire (YPSQ) to complement the Young Schema Questionnaire 3 Short Form (YSQ-S3).

PubMed

Louis, John P; Wood, Alex M; Lockwood, George; Ho, Moon-Ho Ringo; Ferguson, Eamonn

2018-04-19

Negative schemas have been widely recognized as being linked to psychopathology and mental health, and they are central to the Schema Therapy (ST) model. This study is the first to report on the psychometric properties of the Young Positive Schema Questionnaire (YPSQ). In a combined community sample (Manila, Philippines, n = 559; Bangalore, India, n = 350; Singapore, n = 628), we identified a 56-item, 14-factor solution for the YPSQ. Multigroup confirmatory factor analysis supported the 14-factor model using data from two other independent samples: an Eastern sample from Kuala Lumpur, Malaysia (n = 229) and a Western sample from the United States (n = 214). Construct validity was demonstrated with the Young Schema Questionnaire 3 Short Form (YSQ-S3) that measures negative schemas, and divergent validity was demonstrated for 11 of the YPSQ subscales with their respective negative schema counterparts. Convergent validity of the 14 subscales of YPSQ was demonstrated with measures of personality dispositions, emotional distress, well-being, trait gratitude, and humor styles. Positive schemas also showed incremental validity over and above negative schemas for these same measures, thus demonstrating that both positive and negative schemas are separate constructs that relate in unique ways to mental health. Implications for using both the YPSQ and the YSQ-S3 scales in tandem in ST as well as cultural nuances from the use of Asian samples were discussed. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Gstruct: a system for extracting schemas from GML documents

NASA Astrophysics Data System (ADS)

Chen, Hui; Zhu, Fubao; Guan, Jihong; Zhou, Shuigeng

2008-10-01

Geography Markup Language (GML) becomes the de facto standard for geographic information representation on the internet. GML schema provides a way to define the structure, content, and semantic of GML documents. It contains useful structural information of GML documents and plays an important role in storing, querying and analyzing GML data. However, GML schema is not mandatory, and it is common that a GML document contains no schema. In this paper, we present Gstruct, a tool for GML schema extraction. Gstruct finds the features in the input GML documents, identifies geometry datatypes as well as simple datatypes, then integrates all these features and eliminates improper components to output the optimal schema. Experiments demonstrate that Gstruct is effective in extracting semantically meaningful schemas from GML documents.

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…

Adding XML to the MIS Curriculum: Lessons from the Classroom

ERIC Educational Resources Information Center

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

2008-01-01

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

Data Manipulation in an XML-Based Digital Image Library

ERIC Educational Resources Information Center

Chang, Naicheng

2005-01-01

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

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…

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)

Stress leads to aberrant hippocampal involvement when processing schema-related information.

PubMed

Vogel, Susanne; Kluen, Lisa Marieke; Fernández, Guillén; Schwabe, Lars

2018-01-01

Prior knowledge, represented as a mental schema, has critical impact on how we organize, interpret, and process incoming information. Recent findings indicate that the use of an existing schema is coordinated by the medial prefrontal cortex (mPFC), communicating with parietal areas. The hippocampus, however, is crucial for encoding schema-unrelated information but not for schema-related information. A recent study indicated that stress mediators may affect schema-related memory, but the underlying neural mechanisms are currently unknown. Here, we thus tested the impact of acute stress on neural processing of schema-related information. We exposed healthy participants to a stress or control manipulation before they processed, in the MRI scanner, words related or unrelated to a preexisting schema activated by a specific cue. Participants' memory for the presented material was tested 3-5 d after encoding. Overall, the processing of schema-related information activated the mPFC, the precuneus, and the angular gyrus. Stress resulted in aberrant hippocampal activity and connectivity while participants processed schema-related information. This aberrant engagement of the hippocampus was linked to altered subsequent memory. These findings suggest that stress may interfere with the efficient use of prior knowledge during encoding and may have important practical implications, in particular for educational settings. © 2018 Vogel et al.; Published by Cold Spring Harbor Laboratory Press.

The STP (Solar-Terrestrial Physics) Semantic Web based on the RSS1.0 and the RDF

NASA Astrophysics Data System (ADS)

Kubo, T.; Murata, K. T.; Kimura, E.; Ishikura, S.; Shinohara, I.; Kasaba, Y.; Watari, S.; Matsuoka, D.

2006-12-01

In the Solar-Terrestrial Physics (STP), it is pointed out that circulation and utilization of observation data among researchers are insufficient. To archive interdisciplinary researches, we need to overcome this circulation and utilization problems. Under such a background, authors' group has developed a world-wide database that manages meta-data of satellite and ground-based observation data files. It is noted that retrieving meta-data from the observation data and registering them to database have been carried out by hand so far. Our goal is to establish the STP Semantic Web. The Semantic Web provides a common framework that allows a variety of data shared and reused across applications, enterprises, and communities. We also expect that the secondary information related with observations, such as event information and associated news, are also shared over the networks. The most fundamental issue on the establishment is who generates, manages and provides meta-data in the Semantic Web. We developed an automatic meta-data collection system for the observation data using the RSS (RDF Site Summary) 1.0. The RSS1.0 is one of the XML-based markup languages based on the RDF (Resource Description Framework), which is designed for syndicating news and contents of news-like sites. The RSS1.0 is used to describe the STP meta-data, such as data file name, file server address and observation date. To describe the meta-data of the STP beyond RSS1.0 vocabulary, we defined original vocabularies for the STP resources using the RDF Schema. The RDF describes technical terms on the STP along with the Dublin Core Metadata Element Set, which is standard for cross-domain information resource descriptions. Researchers' information on the STP by FOAF, which is known as an RDF/XML vocabulary, creates a machine-readable metadata describing people. Using the RSS1.0 as a meta-data distribution method, the workflow from retrieving meta-data to registering them into the database is automated. This technique is applied for several database systems, such as the DARTS database system and NICT Space Weather Report Service. The DARTS is a science database managed by ISAS/JAXA in Japan. We succeeded in generating and collecting the meta-data automatically for the CDF (Common data Format) data, such as Reimei satellite data, provided by the DARTS. We also create an RDF service for space weather report and real-time global MHD simulation 3D data provided by the NICT. Our Semantic Web system works as follows: The RSS1.0 documents generated on the data sites (ISAS and NICT) are automatically collected by a meta-data collection agent. The RDF documents are registered and the agent extracts meta-data to store them in the Sesame, which is an open source RDF database with support for RDF Schema inferencing and querying. The RDF database provides advanced retrieval processing that has considered property and relation. Finally, the STP Semantic Web provides automatic processing or high level search for the data which are not only for observation data but for space weather news, physical events, technical terms and researches information related to the STP.

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.

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.

Relationships between Childhood Traumatic Experiences, Early Maladaptive Schemas and Interpersonal Styles

PubMed Central

KAYA TEZEL, Fulya; TUTAREL KIŞLAK, Şennur; BOYSAN, Murat

2015-01-01

Introduction Cognitive theories of psychopathology have generally proposed that early experiences of childhood abuse and neglect may result in the development of early maladaptive self-schemas. Maladaptive core schemas are central in the development and maintenance of psychological symptoms in a schema-focused approach. Psychosocial dysfunction in individuals with psychological problems has been consistently found to be associated with symptom severity. However, till date, linkages between psychosocial functioning, early traumatic experiences and core schemas have received little attention. The aim of the present study was to explore the relations among maladaptive interpersonal styles, negative experiences in childhood and core self-schemas in non-clinical adults. Methods A total of 300 adults (58% women) participated in the study. The participants completed a socio-demographic questionnaire, Young Schema Questionnaire, Childhood Trauma Questionnaire and Interpersonal Style Scale. Results Hierarchical regression analyses revealed that the Disconnection and Rejection and Impaired Limits schema domains were significant antecedents of maladaptive interpersonal styles after controlling for demographic characteristics and childhood abuse and neglect. Associations of child sexual abuse with Emotionally Avoidant, Manipulative and Abusive interpersonal styles were mediated by early maladaptive schemas. Early maladaptive schemas mediated the relations of emotional abuse with Emotionally Avoidant and Avoidant interpersonal styles as well as the relations of physical abuse with Avoidant and Abusive interpersonal styles. Conclusion Interpersonal styles in adulthood are significantly associated with childhood traumatic experiences. Significant relations between early traumatic experiences and maladaptive interpersonal styles are mediated by early maladaptive schemas. PMID:28360715

Relationships between Childhood Traumatic Experiences, Early Maladaptive Schemas and Interpersonal Styles.

PubMed

Kaya Tezel, Fulya; Tutarel Kişlak, Şennur; Boysan, Murat

2015-09-01

Cognitive theories of psychopathology have generally proposed that early experiences of childhood abuse and neglect may result in the development of early maladaptive self-schemas. Maladaptive core schemas are central in the development and maintenance of psychological symptoms in a schema-focused approach. Psychosocial dysfunction in individuals with psychological problems has been consistently found to be associated with symptom severity. However, till date, linkages between psychosocial functioning, early traumatic experiences and core schemas have received little attention. The aim of the present study was to explore the relations among maladaptive interpersonal styles, negative experiences in childhood and core self-schemas in non-clinical adults. A total of 300 adults (58% women) participated in the study. The participants completed a socio-demographic questionnaire, Young Schema Questionnaire, Childhood Trauma Questionnaire and Interpersonal Style Scale. Hierarchical regression analyses revealed that the Disconnection and Rejection and Impaired Limits schema domains were significant antecedents of maladaptive interpersonal styles after controlling for demographic characteristics and childhood abuse and neglect. Associations of child sexual abuse with Emotionally Avoidant, Manipulative and Abusive interpersonal styles were mediated by early maladaptive schemas. Early maladaptive schemas mediated the relations of emotional abuse with Emotionally Avoidant and Avoidant interpersonal styles as well as the relations of physical abuse with Avoidant and Abusive interpersonal styles. Interpersonal styles in adulthood are significantly associated with childhood traumatic experiences. Significant relations between early traumatic experiences and maladaptive interpersonal styles are mediated by early maladaptive schemas.

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…

Conceptual Developments in Schema Theory.

ERIC Educational Resources Information Center

Bigenho, Frederick W., Jr.

The conceptual development of schema theory, the way an individual organizes knowledge, is discussed, reviewing a range of perspectives regarding schema. Schema has been defined as the interfacing of incoming information with prior knowledge, clustered in networks. These networks comprise a superordinate concept and supporting information. The…

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

PubMed

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

2013-04-01

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

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

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

The Relation between Trait Mindfulness and Early Maladaptive Schemas in Men Seeking Substance Use Treatment

PubMed Central

Brasfield, Hope; Anderson, Scott; Stuart, Gregory L.

2014-01-01

Recent research has examined the relation between mindfulness and substance use, demonstrating that lower trait mindfulness is associated with increased substance use, and that mindfulness-based interventions help to reduce substance use. Research has also demonstrated that early maladaptive schemas are prevalent among individuals seeking substance use treatment and that targeting early maladaptive schemas in treatment may improve outcomes. However, no known research has examined the relation between mindfulness and early maladaptive schemas despite theoretical and empirical reasons to suspect their association. Therefore, the current study examined the relation between trait mindfulness and early maladaptive schemas among adult men seeking residential substance abuse treatment (N = 82). Findings demonstrated strong negative associations between trait mindfulness and 15 of the 18 early maladaptive schemas. Moreover, men endorsing multiple early maladaptive schemas reported lower trait mindfulness than men with fewer early maladaptive schemas. The implications of these findings for future research and treatment are discussed. PMID:26085852

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

North, Michael J.

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info,more » Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.« less

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.

Extended cooperation in clinical studies through exchange of CDISC metadata between different study software solutions.

PubMed

Kuchinke, W; Wiegelmann, S; Verplancke, P; Ohmann, C

2006-01-01

Our objectives were to analyze the possibility of an exchange of an entire clinical study between two different and independent study software solutions. The question addressed was whether a software-independent transfer of study metadata can be performed without programming efforts and with software routinely used for clinical research. Study metadata was transferred with ODM standard (CDISC). Study software systems employed were MACRO (InferMed) and XTrial (XClinical). For the Proof of Concept, a test study was created with MACRO and exported as ODM. For modification and validation of the ODM export file XML-Spy (Altova) and ODM-Checker (XML4Pharma) were used. Through exchange of a complete clinical study between two different study software solutions, a Proof of Concept of the technical feasibility of a system-independent metadata exchange was conducted successfully. The interchange of study metadata between two different systems at different centers was performed with minimal expenditure. A small number of mistakes had to be corrected in order to generate a syntactically correct ODM file and a "vendor extension" had to be inserted. After these modifications, XTrial exhibited the study, including all data fields, correctly. However, the optical appearance of both CRFs (case report forms) was different. ODM can be used as an exchange format for clinical studies between different study software. Thus, new forms of cooperation through exchange of metadata seem possible, for example the joint creation of electronic study protocols or CRFs at different research centers. Although the ODM standard represents a clinical study completely, it contains no information about the representation of data fields in CRFs.

ECG Rhythm Analysis with Expert and Learner-Generated Schemas in Novice Learners

ERIC Educational Resources Information Center

Blissett, Sarah; Cavalcanti, Rodrigo; Sibbald, Matthew

2015-01-01

Although instruction using expert-generated schemas is associated with higher diagnostic performance, implementation is resource intensive. Learner-generated schemas are an alternative, but may be limited by increases in cognitive load. We compared expert- and learner-generated schemas for learning ECG rhythm interpretation on diagnostic accuracy,…

Thai University Student Schemas and Anxiety Symptomatology

ERIC Educational Resources Information Center

Rhein, Douglas; Sukawatana, Parisa

2015-01-01

This study explores how early maladaptive schemas (EMSs) contribute to the development of anxiety symptomologies among college undergraduates (N = 110). The study was conducted by assessing the correlations between 18 schemas derived from Young's model of Early Maladaptive Schemas (EMSs) and anxiety symptoms using Zung Self-Rating Anxiety Scale…

Schema-Based Text Comprehension

ERIC Educational Resources Information Center

Ensar, Ferhat

2015-01-01

Schema is one of the most common terms used for classifying and constructing knowledge. Therefore, a schema is a pre-planned set of concepts. It usually contains social information and is used to represent chain of events, perceptions, situations, relationships and even objects. For example, Kant initially defines the idea of schema as some…

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.

A Cognitive Therapy Approach to Increasing Father Involvement by Changing Restrictive Masculine Schemas

ERIC Educational Resources Information Center

Mahalik, James R.; Morrison, Jay A.

2006-01-01

Cognitive therapists may be able to help fathers increase their involvement with their children by identifying and changing restrictive masculine schemas that interfere with men's parenting roles. In this paper, we (a) discuss the development of restrictive masculine schemas, (b) explain how these schemas may affect men's involvement in fathering…

The explanatory power of Schema Theory: theoretical foundations and future applications in Ergonomics.

PubMed

Plant, Katherine L; Stanton, Neville A

2013-01-01

Schema Theory is intuitively appealing although it has not always received positive press; critics of the approach argue that the concept is too ambiguous and vague and there are inherent difficulties associated with measuring schemata. As such, the term schema can be met with scepticism and wariness. The purpose of this paper is to address the criticisms that have been levelled at Schema Theory by demonstrating how Schema Theory has been utilised in Ergonomics research, particularly in the key areas of situation awareness, naturalistic decision making and error. The future of Schema Theory is also discussed in light of its potential roles as a unifying theory in Ergonomics and in contributing to our understanding of distributed cognition. We conclude that Schema Theory has made a positive contribution to Ergonomics and with continued refinement of methods to infer and represent schemata it is likely that this trend will continue. This paper reviews the contribution that Schema Theory has made to Ergonomics research. The criticisms of the theory are addressed using examples from the areas of situation awareness, decision making and error.

Inductive creation of an annotation schema for manually indexing clinical conditions from emergency department reports

PubMed Central

Chapman, Wendy W.; Dowling, John N.

2006-01-01

Evaluating automated indexing applications requires comparing automatically indexed terms against manual reference standard annotations. However, there are no standard guidelines for determining which words from a textual document to include in manual annotations, and the vague task can result in substantial variation among manual indexers. We applied grounded theory to emergency department reports to create an annotation schema representing syntactic and semantic variables that could be annotated when indexing clinical conditions. We describe the annotation schema, which includes variables representing medical concepts (e.g., symptom, demographics), linguistic form (e.g., noun, adjective), and modifier types (e.g., anatomic location, severity). We measured the schema’s quality and found: (1) the schema was comprehensive enough to be applied to 20 unseen reports without changes to the schema; (2) agreement between author annotators applying the schema was high, with an F measure of 93%; and (3) an error analysis showed that the authors made complementary errors when applying the schema, demonstrating that the schema incorporates both linguistic and medical expertise. PMID:16230050

Hablo Inglés y Español: Cultural Self-Schemas as a Function of Language.

PubMed

Rodríguez-Arauz, Gloriana; Ramírez-Esparza, Nairán; Pérez-Brena, Norma; Boyd, Ryan L

2017-01-01

Research has demonstrated that bilingual individuals experience a "double personality," which allows them to shift their self-schemas when they are primed with different language modes. In this study, we examine whether self-schemas change in Mexican-American ( N = 193) bilinguals living in the U.S. when they provide open-ended personality self-descriptions in both English and Spanish. We used the Meaning Extraction Helper (MEH) software to extract the most salient self-schemas that influence individuals' self-defining process. Following a qualitative-inductive approach, words were extracted from the open-ended essays and organized into semantic clusters, which were analyzed qualitatively and named. The results show that as expected, language primed bilinguals to think about different self-schemas. In Spanish, their Mexican self-schemas were more salient; whereas, in English their U.S. American self-schemas were more salient. Similarities of self-schemas across languages were assessed using a quantitative approach. Language differences and similarities in theme definition and implications for self-identity of bilinguals are discussed.

Hablo Inglés y Español: Cultural Self-Schemas as a Function of Language

PubMed Central

Rodríguez-Arauz, Gloriana; Ramírez-Esparza, Nairán; Pérez-Brena, Norma; Boyd, Ryan L.

2017-01-01

Research has demonstrated that bilingual individuals experience a “double personality,” which allows them to shift their self-schemas when they are primed with different language modes. In this study, we examine whether self-schemas change in Mexican-American (N = 193) bilinguals living in the U.S. when they provide open-ended personality self-descriptions in both English and Spanish. We used the Meaning Extraction Helper (MEH) software to extract the most salient self-schemas that influence individuals' self-defining process. Following a qualitative-inductive approach, words were extracted from the open-ended essays and organized into semantic clusters, which were analyzed qualitatively and named. The results show that as expected, language primed bilinguals to think about different self-schemas. In Spanish, their Mexican self-schemas were more salient; whereas, in English their U.S. American self-schemas were more salient. Similarities of self-schemas across languages were assessed using a quantitative approach. Language differences and similarities in theme definition and implications for self-identity of bilinguals are discussed. PMID:28611719

Baby Schema in Infant Faces Induces Cuteness Perception and Motivation for Caretaking in Adults.

PubMed

Glocker, Melanie L; Langleben, Daniel D; Ruparel, Kosha; Loughead, James W; Gur, Ruben C; Sachser, Norbert

2009-03-01

Ethologist Konrad Lorenz proposed that baby schema ('Kindchenschema') is a set of infantile physical features such as the large head, round face and big eyes that is perceived as cute and motivates caretaking behavior in other individuals, with the evolutionary function of enhancing offspring survival. Previous work on this fundamental concept was restricted to schematic baby representations or correlative approaches. Here, we experimentally tested the effects of baby schema on the perception of cuteness and the motivation for caretaking using photographs of infant faces. Employing quantitative techniques, we parametrically manipulated the baby schema content to produce infant faces with high (e.g. round face and high forehead), and low (e. g. narrow face and low forehead) baby schema features that retained all the characteristics of a photographic portrait. Undergraduate students (n = 122) rated these infants' cuteness and their motivation to take care of them. The high baby schema infants were rated as more cute and elicited stronger motivation for caretaking than the unmanipulated and the low baby schema infants. This is the first experimental proof of the baby schema effects in actual infant faces. Our findings indicate that the baby schema response is a critical function of human social cognition that may be the basis of caregiving and have implications for infant-caretaker interactions.

[The mediating role of the interpersonal schemas between parenting styles and psychological symptoms: a schema focused view].

PubMed

Soygüt, Gonca; Cakir, Zehra

2009-01-01

The first aim of this study was to examine the relationships between perceived parenting styles and interpersonal schemas. The second purpose was to investigate the mediator role of interpersonal schemas between perceived parenting styles and psychological symptoms. University students (N=94), ages ranging between 17-26, attending to different faculty and classes, have completed Interpersonal Schema Questionnaire, Young Parenting Inventory and Symptom Check List-90. A series of regression analyses revealed that perceived parenting styles have predictive power on a number of interpersonal schemas. Further analyses pointed out that the mediator role of Hostility situation of interpersonal schemas between psychological symptoms and normative, belittling/criticizing, pessimistic/worried parenting styles on the mother forms (Sobel z= 1.94-2.08, p < .01); and normative, belittling/criticizing, emotionally depriving, pessimistic/worried, punitive, and restricted/emotionally inhibited parenting styles (Sobel z= 2.20-2.86, p < .05-.01) on the father forms of the scales. Regression analyses pointed out the predictive power of perceived parenting styles on interpersonal schemas. Moreover, the mediator role of interpersonal schemas between perceived parenting styles and psychological symptoms was also observed. Excluding pessimistic/anxious parenting styles, perceived parenting styles of mothers and fathers differed in their relation to psychological symptoms. In overall evaluation, we believe that, although schemas and parental styles have some universalities in relation to their impacts on psychological health, further research is necessary to address their implications and possible paternal differences in our collectivistic cultural context.

Labeling RDF Graphs for Linear Time and Space Querying

NASA Astrophysics Data System (ADS)

Furche, Tim; Weinzierl, Antonius; Bry, François

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

A conceptual holding model for veterinary applications.

PubMed

Ferrè, Nicola; Kuhn, Werner; Rumor, Massimo; Marangon, Stefano

2014-05-01

Spatial references are required when geographical information systems (GIS) are used for the collection, storage and management of data. In the veterinary domain, the spatial component of a holding (of animals) is usually defined by coordinates, and no other relevant information needs to be interpreted or used for manipulation of the data in the GIS environment provided. Users trying to integrate or reuse spatial data organised in such a way, frequently face the problem of data incompatibility and inconsistency. The root of the problem lies in differences with respect to syntax as well as variations in the semantic, spatial and temporal representations of the geographic features. To overcome these problems and to facilitate the inter-operability of different GIS, spatial data must be defined according to a \\"schema\\" that includes the definition, acquisition, analysis, access, presentation and transfer of such data between different users and systems. We propose an application \\"schema\\" of holdings for GIS applications in the veterinary domain according to the European directive framework (directive 2007/2/EC--INSPIRE). The conceptual model put forward has been developed at two specific levels to produce the essential and the abstract model, respectively. The former establishes the conceptual linkage of the system design to the real world, while the latter describes how the system or software works. The result is an application \\"schema\\" that formalises and unifies the information-theoretic foundations of how to spatially represent a holding in order to ensure straightforward information-sharing within the veterinary community.

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.

Self-Schemas, Depression, and the Processing of Personal Information in Children.

ERIC Educational Resources Information Center

Hammen, Constance; Zupan, Brian A.

1984-01-01

Investigates the applicability of the self-as-schema model to children and examines the extent of negative self-schemas in relatively depressed children among 61 elementary school students; most of the students were between 8 and 12 years old. Results were consistent with the self-as-schema hypotheses, and mood congruent content-specific recall…

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

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

Workplace-based assessment: raters' performance theories and constructs.

PubMed

Govaerts, M J B; Van de Wiel, M W J; Schuwirth, L W T; Van der Vleuten, C P M; Muijtjens, A M M

2013-08-01

Weaknesses in the nature of rater judgments are generally considered to compromise the utility of workplace-based assessment (WBA). In order to gain insight into the underpinnings of rater behaviours, we investigated how raters form impressions of and make judgments on trainee performance. Using theoretical frameworks of social cognition and person perception, we explored raters' implicit performance theories, use of task-specific performance schemas and the formation of person schemas during WBA. We used think-aloud procedures and verbal protocol analysis to investigate schema-based processing by experienced (N = 18) and inexperienced (N = 16) raters (supervisor-raters in general practice residency training). Qualitative data analysis was used to explore schema content and usage. We quantitatively assessed rater idiosyncrasy in the use of performance schemas and we investigated effects of rater expertise on the use of (task-specific) performance schemas. Raters used different schemas in judging trainee performance. We developed a normative performance theory comprising seventeen inter-related performance dimensions. Levels of rater idiosyncrasy were substantial and unrelated to rater expertise. Experienced raters made significantly more use of task-specific performance schemas compared to inexperienced raters, suggesting more differentiated performance schemas in experienced raters. Most raters started to develop person schemas the moment they began to observe trainee performance. The findings further our understanding of processes underpinning judgment and decision making in WBA. Raters make and justify judgments based on personal theories and performance constructs. Raters' information processing seems to be affected by differences in rater expertise. The results of this study can help to improve rater training, the design of assessment instruments and decision making in WBA.

Sexual Self Schema as a Moderator of Sexual and Psychological Outcomes for Gynecologic Cancer Survivors

PubMed Central

Andersen, Barbara L.; Fowler, Jeffrey M.; Maxwell, G. Larry

2008-01-01

Abstract Gynecologic cancer patients are at high risk for emotional distress and sexual dysfunction. The present study tested sexual self schema as an individual difference variable that might be useful in identifying those at risk for unfavorable outcomes. First, we tested schema as a predictor of sexual outcomes,including bodychangestress. Second,we examined schema as a contributor to broader quality of life outcomes, specifically as a moderator of the relationship between sexual satisfaction and psychological statue (depressive symptoms and quality of life). A cross-sectional design was used. Gynecologic cancer survivors (N = 175) 2−10 years post treatment were assessed during routine follow up. In regression analyses controlling for sociodemographic variables, patients' physical symptoms/signs as evaluated by nurses, health status, and extent of partner sexual difficulties, sexual self schema accounted for significant variance in the prediction of current sexual behavior, responsiveness, and satisfaction. Moreover, schema moderated the relationship between sexual satisfaction and psychological outcomes, suggesting that a positive sexual self schema might “buffer” patients from depressive symptoms when their sexual satisfaction is low. Furthermore, the combination of a negative sexual self schema and low sexual satisfaction might heighten survivors' risk for psychological distress, including depressive symptomatology. These data support the consideration of sexual self schema as a predictor of sexual morbidity among gynecologic cancer survivors. PMID:18418707

Evaluation of optimized b-value sampling schemas for diffusion kurtosis imaging with an application to stroke patient data

PubMed Central

Yan, Xu; Zhou, Minxiong; Ying, Lingfang; Yin, Dazhi; Fan, Mingxia; Yang, Guang; Zhou, Yongdi; Song, Fan; Xu, Dongrong

2013-01-01

Diffusion kurtosis imaging (DKI) is a new method of magnetic resonance imaging (MRI) that provides non-Gaussian information that is not available in conventional diffusion tensor imaging (DTI). DKI requires data acquisition at multiple b-values for parameter estimation; this process is usually time-consuming. Therefore, fewer b-values are preferable to expedite acquisition. In this study, we carefully evaluated various acquisition schemas using different numbers and combinations of b-values. Acquisition schemas that sampled b-values that were distributed to two ends were optimized. Compared to conventional schemas using equally spaced b-values (ESB), optimized schemas require fewer b-values to minimize fitting errors in parameter estimation and may thus significantly reduce scanning time. Following a ranked list of optimized schemas resulted from the evaluation, we recommend the 3b schema based on its estimation accuracy and time efficiency, which needs data from only 3 b-values at 0, around 800 and around 2600 s/mm2, respectively. Analyses using voxel-based analysis (VBA) and region-of-interest (ROI) analysis with human DKI datasets support the use of the optimized 3b (0, 1000, 2500 s/mm2) DKI schema in practical clinical applications. PMID:23735303

Early Maladaptive Schemas and Aggression in Men Seeking Residential Substance Use Treatment

PubMed Central

Shorey, Ryan C.; Elmquist, Joanna; Anderson, Scott; Stuart, Gregory L.

2015-01-01

Social-cognitive theories of aggression postulate that individuals who perpetrate aggression are likely to have high levels of maladaptive cognitive schemas that increase risk for aggression. Indeed, recent research has begun to examine whether early maladaptive schemas may increase the risk for aggression. However, no known research has examined this among individuals in substance use treatment, despite aggression and early maladaptive schemas being more prevalent among individuals with a substance use disorder than the general population. Toward this end, we examined the relationship between early maladaptive schemas and aggression in men in a residential substance use treatment facility (N = 106). Utilizing pre-existing patient records, results demonstrated unique associations between early maladaptive schema domains and aggression depending on the type of aggression and schema domain examined, even after controlling for substance use, antisocial personality, age, and education. The Impaired Limits domain was positively associated with verbal aggression, aggressive attitude, and overall aggression, whereas the Disconnection and Rejection domain was positively associated with physical aggression. These findings are consistent with social-cognitive models of aggression and advance our understanding of how early maladaptive schemas may influence aggression. The implications of these findings for future research are discussed. PMID:25897180

Integration of Schemas on the Pre-Design Level Using the KCPM-Approach

NASA Astrophysics Data System (ADS)

Vöhringer, Jürgen; Mayr, Heinrich C.

Integration is a central research and operational issue in information system design and development. It can be conducted on the system, schema, and view or data level. On the system level, integration deals with the progressive linking and testing of system components to merge their functional and technical characteristics and behavior into a comprehensive, interoperable system. Schema integration comprises the comparison and merging of two or more schemas, usually conceptual database schemas. The integration of data deals with merging the contents of multiple sources of related data. View integration is similar to schema integration, however focuses on views and queries on these instead of schemas. All these types of integration have in common, that two or more sources are merged and previously compared, in order to identify matches and mismatches as well as conflicts and inconsistencies. The sources may stem from heterogeneous companies, organizational units or projects. Integration enables the reuse and combined use of source components.

Maladaptive schemas as mediators of the relationship between previous victimizations in the family and dating violence victimization in adolescents.

PubMed

Calvete, Esther; Gámez-Guadix, Manuel; Fernández-Gonzalez, Liria; Orue, Izaskun; Borrajo, Erika

2018-07-01

This study examined whether exposure to family violence, both in the form of direct victimization and witnessing violence, predicted dating violence victimization in adolescents through maladaptive schemas. A sample of 933 adolescents (445 boys and 488 girls), aged between 13 and 18 (M = 15.10), participated in a three-year longitudinal study. They completed measures of exposure to family violence, maladaptive schemas of disconnection/rejection, and dating violence victimization. The findings indicate that witnessing family violence predicts the increase of dating violence victimization over time, through the mediation of maladaptive schemas in girls, but not in boys. Direct victimization in the family predicts dating violence victimization directly, without the mediation of schemas. In addition, maladaptive schemas contribute to the perpetuation of dating violence victimization over time. These findings provide new opportunities for preventive interventions, as maladaptive schemas can be modified. Copyright © 2018 Elsevier Ltd. All rights reserved.

Partitioning an object-oriented terminology schema.

PubMed

Gu, H; Perl, Y; Halper, M; Geller, J; Kuo, F; Cimino, J J

2001-07-01

Controlled medical terminologies are increasingly becoming strategic components of various healthcare enterprises. However, the typical medical terminology can be difficult to exploit due to its extensive size and high density. The schema of a medical terminology offered by an object-oriented representation is a valuable tool in providing an abstract view of the terminology, enhancing comprehensibility and making it more usable. However, schemas themselves can be large and unwieldy. We present a methodology for partitioning a medical terminology schema into manageably sized fragments that promote increased comprehension. Our methodology has a refinement process for the subclass hierarchy of the terminology schema. The methodology is carried out by a medical domain expert in conjunction with a computer. The expert is guided by a set of three modeling rules, which guarantee that the resulting partitioned schema consists of a forest of trees. This makes it easier to understand and consequently use the medical terminology. The application of our methodology to the schema of the Medical Entities Dictionary (MED) is presented.

Relationship of negative self-schemas and attachment styles with appearance schemas.

PubMed

Ledoux, Tracey; Winterowd, Carrie; Richardson, Tamara; Clark, Julie Dorton

2010-06-01

The purpose was to test, among women, the relationship between negative self-schemas and styles of attachment with men and women and two types of appearance investment (Self-evaluative and Motivational Salience). Predominantly Caucasian undergraduate women (N=194) completed a modified version of the Relationship Questionnaire, the Young Schema Questionnaire-Short Form, and the Appearance Schemas Inventory-Revised. Linear multiple regression analyses were conducted with Motivational Salience and Self-evaluative Salience of appearance serving as dependent variables and relevant demographic variables, negative self-schemas, and styles of attachment to men serving as independent variables. Styles of attachment to women were not entered into these regression models because Pearson correlations indicated they were not related to either dependent variable. Self-evaluative Salience of appearance was related to impaired autonomy and performance negative self-schema and the preoccupation style of attachment with men, while Motivational Salience of appearance was related only to the preoccupation style of attachment with men. 2010 Elsevier Ltd. All rights reserved.

Neural mechanisms of mental schema: a triplet of delta, low beta/spindle and ripple oscillations.

PubMed

Ohki, Takefumi; Takei, Yuichi

2018-02-06

Schemas are higher-level knowledge structures that integrate and organise lower-level representations. As internal templates, schemas are formed according to how events are perceived, interpreted and remembered. Although these higher-level units are assumed to play a fundamental role in our daily life from an early age, the neuronal basis and mechanisms of schema formation and use remain largely unknown. It is important to elucidate how the brain constructs and maintains these higher-level units. In order to examine the possible neural underpinnings of schema, we recapitulate previous work and discuss their findings related to schemas as the brain template. We specifically focused on low beta/spindle oscillations, which are assumed to be the key components of schemas, and propose that the brain template is implemented with a triplet of neural oscillations, that is delta, low beta/spindle and ripple oscillations. © 2018 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Role of Father–Child Relational Quality in Early Maladaptive Schemas

PubMed Central

Monirpoor, Nader; Gholamyzarch, Morteza; Tamaddonfard, Mohsen; Khoosfi, Helen; Ganjali, Ali Reza

2012-01-01

Background Primary maladaptive schemas, which are the basis of high-risk behavior and psychological disorders, result from childhood experiences with significant objects, such as fathers, in different developmental phases. Objectives This endeavor examined the role of the father in predicting these schemas. Patients and Methods A total of 345 Islamic Azad University students (Qom Branch) who were chosen through convenience sampling completed the Young Schema Questionnaire, the Parental Bonding Instrument, and the Parent–Child Relationship Survey. Results A multivariate regression analysis indicated that anumber of aspects of the father–child relationship, including care, emotional interaction, positive affection, the effective relationship, and excessive support, predict particular schemas. Conclusions Therefore, these findings suggested that psychotherapists examine the different aspects of the father–child relationship when restructuring schemas. PMID:24971232

The Relation Between Antisocial and Borderline Personality Symptoms and Early Maladaptive Schemas in a Treatment Seeking Sample of Male Substance Users

PubMed Central

Shorey, Ryan C.; Anderson, Scott; Stuart, Gregory L.

2014-01-01

Individuals with substance use disorders are more likely to have antisocial and borderline personality disorder than non-substance abusers. Recently, research has examined the relations between early maladaptive schemas and personality disorders, as early maladaptive schemas are believed to underlie personality disorders. However, there is a dearth of research on the relations between early maladaptive schemas and personality disorders among individuals seeking treatment for substance abuse. The current study examined the relations among early maladaptive schemas and antisocial and borderline personality within in a sample of men seeking substance abuse treatment (n = 98). Results demonstrated that early maladaptive schema domains were associated with antisocial and borderline personality symptoms. Implications of these findings for substance use treatment and research are discussed. PMID:23650153

Explaining sex differences in managerial career satisfier preferences: the role of gender self-schema.

PubMed

Eddleston, Kimberly A; Veiga, John F; Powell, Gary N

2006-03-01

Using survey data from 400 managers, the authors examined whether gender self-schema would explain sex differences in preferences for status-based and socioemotional career satisfiers. Female gender self-schema, represented by femininity and family role salience, completely mediated the relationship between managers' sex and preferences for socioemotional career satisfiers. However, male gender self-schema, represented by masculinity and career role salience, did not mediate the relationship between managers' sex and preferences for status-based career satisfiers. As expected, male managers regarded status-based career satisfiers as more important and socioemotional career satisfiers as less important than female managers did. The proposed conceptualization of male and female gender self-schemas, which was supported by the data, enhances understanding of adult self-schema and work-related attitudes and behavior.

Community-Based Development of Standards for Geochemical and Geochronological Data

NASA Astrophysics Data System (ADS)

Lehnert, K. A.; Walker, D.; Vinay, S.; Djapic, B.; Ash, J.; Falk, B.

2007-12-01

The Geoinformatics for Geochemistry (GfG) Program (www.geoinfogeochem.org) and the EarthChem project (www.earthchem.org) aim to maximize the application of geochemical data in Geoscience research and education by building a new advanced data infrastructure for geochemistry that facilitates the compilation, communication, serving, and visualization of geochemical data and their integration with the broad Geoscience data set. Building this new data infrastructure poses substantial challenges that are primarily cultural in nature, and require broad community involvement in the development and implementation of standards for data reporting (e.g., metadata for analytical procedures, data quality, and analyzed samples), data publication, and data citation to achieve broad acceptance and use. Working closely with the science community, with professional societies, and with editors and publishers, recommendations for standards for the reporting of geochemical and geochronological data in publications and to data repositories have been established, which are now under consideration for adoption in journal and agency policies. The recommended standards are aligned with the GfG and EarthChem data models as well as the EarthChem XML schema for geochemical data. Through partnerships with other national and international data management efforts in geochemistry and in the broader marine and terrestrial geosciences, GfG and EarthChem seek to integrate their development of geochemical metadata standards, data format, and semantics with relevant existing and emerging standards and ensure compatibility and compliance.

Data dictionary services in XNAT and the Human Connectome Project.

PubMed

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J; Marcus, Daniel S

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures.

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction.

PubMed

Hill, Jon; Davis, Katie E

2014-01-01

Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work.

Data dictionary services in XNAT and the Human Connectome Project

PubMed Central

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J.; Marcus, Daniel S.

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures. PMID:25071542

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

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.

The SGML Standardization Framework and the Introduction of XML

PubMed Central

Grütter, Rolf

2000-01-01

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

The SGML standardization framework and the introduction of XML.

PubMed

Fierz, W; Grütter, R

2000-01-01

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

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

NASA Astrophysics Data System (ADS)

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

1999-05-01

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

A Platform to Build Mobile Health Apps: The Personal Health Intervention Toolkit (PHIT).

PubMed

Eckhoff, Randall Peter; Kizakevich, Paul Nicholas; Bakalov, Vesselina; Zhang, Yuying; Bryant, Stephanie Patrice; Hobbs, Maria Ann

2015-06-01

Personal Health Intervention Toolkit (PHIT) is an advanced cross-platform software framework targeted at personal self-help research on mobile devices. Following the subjective and objective measurement, assessment, and plan methodology for health assessment and intervention recommendations, the PHIT platform lets researchers quickly build mobile health research Android and iOS apps. They can (1) create complex data-collection instruments using a simple extensible markup language (XML) schema; (2) use Bluetooth wireless sensors; (3) create targeted self-help interventions based on collected data via XML-coded logic; (4) facilitate cross-study reuse from the library of existing instruments and interventions such as stress, anxiety, sleep quality, and substance abuse; and (5) monitor longitudinal intervention studies via daily upload to a Web-based dashboard portal. For physiological data, Bluetooth sensors collect real-time data with on-device processing. For example, using the BinarHeartSensor, the PHIT platform processes the heart rate data into heart rate variability measures, and plots these data as time-series waveforms. Subjective data instruments are user data-entry screens, comprising a series of forms with validation and processing logic. The PHIT instrument library consists of over 70 reusable instruments for various domains including cognitive, environmental, psychiatric, psychosocial, and substance abuse. Many are standardized instruments, such as the Alcohol Use Disorder Identification Test, Patient Health Questionnaire-8, and Post-Traumatic Stress Disorder Checklist. Autonomous instruments such as battery and global positioning system location support continuous background data collection. All data are acquired using a schedule appropriate to the app's deployment. The PHIT intelligent virtual advisor (iVA) is an expert system logic layer, which analyzes the data in real time on the device. This data analysis results in a tailored app of interventions and other data-collection instruments. For example, if a user anxiety score exceeds a threshold, the iVA might add a meditation intervention to the task list in order to teach the user how to relax, and schedule a reassessment using the anxiety instrument 2 weeks later to re-evaluate. If the anxiety score exceeds a higher threshold, then an advisory to seek professional help would be displayed. Using the easy-to-use PHIT scripting language, the researcher can program new instruments, the iVA, and interventions to their domain-specific needs. The iVA, instruments, and interventions are defined via XML files, which facilities rapid app development and deployment. The PHIT Web-based dashboard portal provides the researcher access to all the uploaded data. After a secure login, the data can be filtered by criteria such as study, protocol, domain, and user. Data can also be exported into a comma-delimited file for further processing. The PHIT framework has proven to be an extensible, reconfigurable technology that facilitates mobile data collection and health intervention research. Additional plans include instrument development in other domains, additional health sensors, and a text messaging notification system.

A Platform to Build Mobile Health Apps: The Personal Health Intervention Toolkit (PHIT)

PubMed Central

2015-01-01

Personal Health Intervention Toolkit (PHIT) is an advanced cross-platform software framework targeted at personal self-help research on mobile devices. Following the subjective and objective measurement, assessment, and plan methodology for health assessment and intervention recommendations, the PHIT platform lets researchers quickly build mobile health research Android and iOS apps. They can (1) create complex data-collection instruments using a simple extensible markup language (XML) schema; (2) use Bluetooth wireless sensors; (3) create targeted self-help interventions based on collected data via XML-coded logic; (4) facilitate cross-study reuse from the library of existing instruments and interventions such as stress, anxiety, sleep quality, and substance abuse; and (5) monitor longitudinal intervention studies via daily upload to a Web-based dashboard portal. For physiological data, Bluetooth sensors collect real-time data with on-device processing. For example, using the BinarHeartSensor, the PHIT platform processes the heart rate data into heart rate variability measures, and plots these data as time-series waveforms. Subjective data instruments are user data-entry screens, comprising a series of forms with validation and processing logic. The PHIT instrument library consists of over 70 reusable instruments for various domains including cognitive, environmental, psychiatric, psychosocial, and substance abuse. Many are standardized instruments, such as the Alcohol Use Disorder Identification Test, Patient Health Questionnaire-8, and Post-Traumatic Stress Disorder Checklist. Autonomous instruments such as battery and global positioning system location support continuous background data collection. All data are acquired using a schedule appropriate to the app’s deployment. The PHIT intelligent virtual advisor (iVA) is an expert system logic layer, which analyzes the data in real time on the device. This data analysis results in a tailored app of interventions and other data-collection instruments. For example, if a user anxiety score exceeds a threshold, the iVA might add a meditation intervention to the task list in order to teach the user how to relax, and schedule a reassessment using the anxiety instrument 2 weeks later to re-evaluate. If the anxiety score exceeds a higher threshold, then an advisory to seek professional help would be displayed. Using the easy-to-use PHIT scripting language, the researcher can program new instruments, the iVA, and interventions to their domain-specific needs. The iVA, instruments, and interventions are defined via XML files, which facilities rapid app development and deployment. The PHIT Web-based dashboard portal provides the researcher access to all the uploaded data. After a secure login, the data can be filtered by criteria such as study, protocol, domain, and user. Data can also be exported into a comma-delimited file for further processing. The PHIT framework has proven to be an extensible, reconfigurable technology that facilitates mobile data collection and health intervention research. Additional plans include instrument development in other domains, additional health sensors, and a text messaging notification system. PMID:26033047

SciFlo: Semantically-Enabled Grid Workflow for Collaborative Science

NASA Astrophysics Data System (ADS)

Yunck, T.; Wilson, B. D.; Raskin, R.; Manipon, G.

2005-12-01

SciFlo is a system for Scientific Knowledge Creation on the Grid using a Semantically-Enabled Dataflow Execution Environment. SciFlo leverages Simple Object Access Protocol (SOAP) Web Services and the Grid Computing standards (WS-* standards and the Globus Alliance toolkits), and enables scientists to do multi-instrument Earth Science by assembling reusable SOAP Services, native executables, local command-line scripts, and python codes into a distributed computing flow (a graph of operators). SciFlo's XML dataflow documents can be a mixture of concrete operators (fully bound operations) and abstract template operators (late binding via semantic lookup). All data objects and operators can be both simply typed (simple and complex types in XML schema) and semantically typed using controlled vocabularies (linked to OWL ontologies such as SWEET). By exploiting ontology-enhanced search and inference, one can discover (and automatically invoke) Web Services and operators that have been semantically labeled as performing the desired transformation, and adapt a particular invocation to the proper interface (number, types, and meaning of inputs and outputs). The SciFlo client & server engines optimize the execution of such distributed data flows and allow the user to transparently find and use datasets and operators without worrying about the actual location of the Grid resources. The scientist injects a distributed computation into the Grid by simply filling out an HTML form or directly authoring the underlying XML dataflow document, and results are returned directly to the scientist's desktop. A Visual Programming tool is also being developed, but it is not required. Once an analysis has been specified for a granule or day of data, it can be easily repeated with different control parameters and over months or years of data. SciFlo uses and preserves semantics, and also generates and infers new semantic annotations. Specifically, the SciFlo engine uses semantic metadata to understand (infer) what it is doing and potentially improve the data flow; preserves semantics by saving links to the semantics of (metadata describing) the input datasets, related datasets, and the data transformations (algorithms) used to generate downstream products; generates new metadata by allowing the user to add semantic annotations to the generated data products (or simply accept automatically generated provenance annotations); and infers new semantic metadata by understanding and applying logic to the semantics of the data and the transformations performed. Much ontology development still needs to be done but, nevertheless, SciFlo documents provide a substrate for using and preserving more semantics as ontologies develop. We will give a live demonstration of the growing SciFlo network using an example dataflow in which atmospheric temperature and water vapor profiles from three Earth Observing System (EOS) instruments are retrieved using SOAP (geo-location query & data access) services, co-registered, and visually & statistically compared on demand (see http://sciflo.jpl.nasa.gov for more information).

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

Sleep Spindle Density Predicts the Effect of Prior Knowledge on Memory Consolidation

PubMed Central

Lambon Ralph, Matthew A.; Kempkes, Marleen; Cousins, James N.; Lewis, Penelope A.

2016-01-01

Information that relates to a prior knowledge schema is remembered better and consolidates more rapidly than information that does not. Another factor that influences memory consolidation is sleep and growing evidence suggests that sleep-related processing is important for integration with existing knowledge. Here, we perform an examination of how sleep-related mechanisms interact with schema-dependent memory advantage. Participants first established a schema over 2 weeks. Next, they encoded new facts, which were either related to the schema or completely unrelated. After a 24 h retention interval, including a night of sleep, which we monitored with polysomnography, participants encoded a second set of facts. Finally, memory for all facts was tested in a functional magnetic resonance imaging scanner. Behaviorally, sleep spindle density predicted an increase of the schema benefit to memory across the retention interval. Higher spindle densities were associated with reduced decay of schema-related memories. Functionally, spindle density predicted increased disengagement of the hippocampus across 24 h for schema-related memories only. Together, these results suggest that sleep spindle activity is associated with the effect of prior knowledge on memory consolidation. SIGNIFICANCE STATEMENT Episodic memories are gradually assimilated into long-term memory and this process is strongly influenced by sleep. The consolidation of new information is also influenced by its relationship to existing knowledge structures, or schemas, but the role of sleep in such schema-related consolidation is unknown. We show that sleep spindle density predicts the extent to which schemas influence the consolidation of related facts. This is the first evidence that sleep is associated with the interaction between prior knowledge and long-term memory formation. PMID:27030764

XGI: a graphical interface for XQuery creation.

PubMed

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

2007-10-11

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

A Services-Oriented Architecture for Water Observations Data

NASA Astrophysics Data System (ADS)

Maidment, D. R.; Zaslavsky, I.; Valentine, D.; Tarboton, D. G.; Whitenack, T.; Whiteaker, T.; Hooper, R.; Kirschtel, D.

2009-04-01

Water observations data are time series of measurements made at point locations of water level, flow, and quality and corresponding data for climatic observations at point locations such as gaged precipitation and weather variables. A services-oriented architecture has been built for such information for the United States that has three components: hydrologic information servers, hydrologic information clients, and a centralized metadata cataloging system. These are connected using web services for observations data and metadata defined by an XML-based language called WaterML. A Hydrologic Information Server can be built by storing observations data in a relational database schema in the CUAHSI Observations Data Model, in which case, web services access to the data and metadata is automatically provided by query functions for WaterML that are wrapped around the relational database within a web server. A Hydrologic Information Server can also be constructed by custom-programming an interface to an existing water agency web site so that responds to the same queries by producing data in WaterML as do the CUAHSI Observations Data Model based servers. A Hydrologic Information Client is one which can interpret and ingest WaterML metadata and data. We have two client applications for Excel and ArcGIS and have shown how WaterML web services can be ingested into programming environments such as Matlab and Visual Basic. HIS Central, maintained at the San Diego Supercomputer Center is a repository of observational metadata for WaterML web services which presently indexes 342 million data measured at 1.75 million locations. This is the largest catalog water observational data for the United States presently in existence. As more observation networks join what we term "CUAHSI Water Data Federation", and the system accommodates a growing number of sites, measured parameters, applications, and users, rapid and reliable access to large heterogeneous hydrologic data repositories becomes critical. The CUAHSI HIS solution to the scalability and heterogeneity challenges has several components. Structural differences across the data repositories are addressed by building a standard services foundation for the exchange of hydrologic data, as derived from a common information model for observational data measured at stationary points and its implementation as a relational schema (ODM) and an XML schema (WaterML). Semantic heterogeneity is managed by mapping water quantity, water quality, and other parameters collected by government agencies and academic projects to a common ontology. The WaterML-compliant web services are indexed in a community services registry called HIS Central (hiscentral.cuahsi.org). Once a web service is registered in HIS Central, its metadata (site and variable characteristics, period of record for each variable at each site, etc.) is harvested and appended to the central catalog. The catalog is further updated as the service publisher associates the variables in the published service with ontology concepts. After this, the newly published service becomes available for spatial and semantics-based queries from online and desktop client applications developed by the project. Hydrologic system server software is now deployed at more than a dozen locations in the United States and Australia. To provide rapid access to data summaries, in particular for several nation-wide data repositories including EPA STORET, USGS NWIS, and USDA SNOTEL, we convert the observation data catalogs and databases with harvested data values into special representations that support high-performance analysis and visualization. The construction of OLAP (Online Analytical Processing) cubes, often called data cubes, is an approach to organizing and querying large multi-dimensional data collections. We have applied the OLAP techniques, as implemented in Microsoft SQL Server 2005/2008, to the analysis of the catalogs from several agencies. OLAP analysis results reflect geography and history of observation data availability from USGS NWIS, EPA STORET, and USDA SNOTEL repositories, and spatial and temporal dynamics of the available measurements for several key nutrient-related parameters. Our experience developing the CUAHSI HIS cyberinfrastructure demonstrated that efficient integration of hydrologic observations from multiple government and academic sources requires a range of technical approaches focused on managing different components of data heterogeneity and system scalability. While this submission addresses technical aspects of developing a national-scale information system for hydrologic observations, the challenges of explicating shared semantics of hydrologic observations and building a community of HIS users and developers remain critical in constructing a nation-wide federation of water data services.

10 years experience with pioneering open access publishing in health informatics: the Journal of Medical Internet Research (JMIR).

PubMed

Eysenbach, Gunther

2010-01-01

Peer-reviewed journals remain important vehicles for knowledge transfer and dissemination in health informatics, yet, their format, processes and business models are changing only slowly. Up to the end of last century, it was common for individual researchers and scientific organizations to leave the business of knowledge transfer to professional publishers, signing away their rights to the works in the process, which in turn impeded wider dissemination. Traditional medical informatics journals are poorly cited and the visibility and uptake of articles beyond the medical informatics community remain limited. In 1999, the Journal of Medical Internet Research (JMIR; http://www.jmir.org) was launched, featuring several innovations including 1) ownership and copyright retained by the authors, 2) electronic-only, "lean" non-for-profit publishing, 3) openly accessible articles with a reversed business model (author pays instead of reader pays), 4) technological innovations such as automatic XML tagging and reference checking, on-the-fly PDF generation from XML, etc., enabling wide distribution in various bibliographic and full-text databases. In the past 10 years, despite limited resources, the journal has emerged as a leading journal in health informatics, and is presently ranked the top journal in the medical informatics and health services research categories by impact factor. The paper summarizes some of the features of the Journal, and uses bibliometric and access data to compare the influence of the Journal on the discipline of medical informatics and other disciplines. While traditional medical informatics journals are primarily cited by other Medical Informatics journals (33%-46% of citations), JMIR papers are to a more often cited by "end-users" (policy, public health, clinical journals), which may be partly attributable to the "open access advantage".

Effects of Preventative Tutoring on the Mathematical Problem Solving of Third-Grade Students With Math and Reading Difficulties.

PubMed

Fuchs, Lynn S; Seethaler, Pamela M; Powell, Sarah R; Fuchs, Douglas; Hamlett, Carol L; Fletcher, Jack M

2008-01-01

This study assessed the effects of preventative tutoring on the math problem solving of third-grade students with math and reading difficulties. Students (n = 35) were assigned randomly to continue in their general education math program or to receive secondary preventative tutoring 3 times per week, 30 min per session, for 12 weeks. Schema-broadening tutoring taught students to (a) focus on the mathematical structure of 3 problem types; (b) recognize problems as belonging to those 3 problem-type schemas; (c) solve the 3 word-problem types; and (d) transfer solution methods to problems that include irrelevant information, 2-digit operands, missing information in the first or second positions in the algebraic equation, or relevant information in charts, graphs, and pictures. Also, students were taught to perform the calculation and algebraic skills foundational for problem solving. Analyses of variance revealed statistically significant effects on a wide range of word problems, with large effect sizes. Findings support the efficacy of the tutoring protocol for preventing word-problem deficits among third-grade students with math and reading deficits.

Effects of Preventative Tutoring on the Mathematical Problem Solving of Third-Grade Students With Math and Reading Difficulties

PubMed Central

Fuchs, Lynn S.; Seethaler, Pamela M.; Powell, Sarah R.; Fuchs, Douglas; Hamlett, Carol L.; Fletcher, Jack M.

2009-01-01

This study assessed the effects of preventative tutoring on the math problem solving of third-grade students with math and reading difficulties. Students (n = 35) were assigned randomly to continue in their general education math program or to receive secondary preventative tutoring 3 times per week, 30 min per session, for 12 weeks. Schema-broadening tutoring taught students to (a) focus on the mathematical structure of 3 problem types; (b) recognize problems as belonging to those 3 problem-type schemas; (c) solve the 3 word-problem types; and (d) transfer solution methods to problems that include irrelevant information, 2-digit operands, missing information in the first or second positions in the algebraic equation, or relevant information in charts, graphs, and pictures. Also, students were taught to perform the calculation and algebraic skills foundational for problem solving. Analyses of variance revealed statistically significant effects on a wide range of word problems, with large effect sizes. Findings support the efficacy of the tutoring protocol for preventing word-problem deficits among third-grade students with math and reading deficits. PMID:20209074

Exploring revictimization process among Turkish women: The role of early maladaptive schemas on the link between child abuse and partner violence.

PubMed

Atmaca, Sinem; Gençöz, Tülin

2016-02-01

The purpose of the current study is to explore the revictimization process between child abuse and neglect (CAN), and intimate partner violence (IPV) based on the schema theory perspective. For this aim, 222 married women recruited in four central cities of Turkey participated in the study. Results indicated that early negative CAN experiences increased the risk of being exposed to later IPV. Specifically, emotional abuse and sexual abuse in the childhood predicted the four subtypes of IPV, which are physical, psychological, and sexual violence, and injury, while physical abuse only associated with physical violence. To explore the mediational role of early maladaptive schemas (EMSs) on this association, first, five schema domains were tested via Parallel Multiple Mediation Model. Results indicated that only Disconnection/Rejection (D/R) schema domains mediated the association between CAN and IPV. Second, to determine the particular mediational roles of each schema, eighteen EMS were tested as mediators, and results showed that Emotional Deprivation Schema and Vulnerability to Harm or Illness Schema mediated the association between CAN and IPV. These findings provided an empirical support for the crucial roles of EMSs on the effect of revictimization process. Clinical implications were discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Integrated Design and Production Reference Integration with ArchGenXML V1.00

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

Barter, R H

2004-07-20

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

PDF for Healthcare and Child Health Data Forms.

PubMed

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

2008-11-06

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

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

DTIC Science & Technology

2003-09-01

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

Catalog Descriptions Using VOTable Files

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

Correlates of African American Men's Sexual Schemas

PubMed Central

Morales, Dawn A.; Coyne-Beasley, Tamera; St. Lawrence, Janet

2013-01-01

Sexual schemas are cognitive representations of oneself as a sexual being and aid in the processing of sexually relevant information. We examined the relationship between sociosexuality (attitudes about casual sex), masculine ideology (attitudes toward traditional men and male roles), and cultural centrality (strength of identity with racial group) as significant psychosocial and sociocultural predictors in shaping young, heterosexual African American men's sexual schemas. A community sample (n=133) of men in a southeastern city of the United States completed quantitative self-report measures examining their attitudes and behavior related to casual sex, beliefs about masculinity, racial and cultural identity, and self-views of various sexual aspects of themselves. Results indicated that masculine ideology and cultural centrality were both positively related to men's sexual schemas. Cultural centrality explained 12 % of the variance in level of sexual schema, and had the strongest correlation of the predictor variables with sexual schema (r=.36). The need for more attention to the bidirectional relationships between masculinity, racial/cultural identity, and sexual schemas in prevention, intervention, and public health efforts for African American men is discussed. PMID:24031118

The acquisition process of musical tonal schema: implications from connectionist modeling.

PubMed

Matsunaga, Rie; Hartono, Pitoyo; Abe, Jun-Ichi

2015-01-01

Using connectionist modeling, we address fundamental questions concerning the acquisition process of musical tonal schema of listeners. Compared to models of previous studies, our connectionist model (Learning Network for Tonal Schema, LeNTS) was better equipped to fulfill three basic requirements. Specifically, LeNTS was equipped with a learning mechanism, bound by culture-general properties, and trained by sufficient melody materials. When exposed to Western music, LeNTS acquired musical 'scale' sensitivity early and 'harmony' sensitivity later. The order of acquisition of scale and harmony sensitivities shown by LeNTS was consistent with the culture-specific acquisition order shown by musically westernized children. The implications of these results for the acquisition process of a tonal schema of listeners are as follows: (a) the acquisition process may entail small and incremental changes, rather than large and stage-like changes, in corresponding neural circuits; (b) the speed of schema acquisition may mainly depend on musical experiences rather than maturation; and (c) the learning principles of schema acquisition may be culturally invariant while the acquired tonal schemas are varied with exposed culture-specific music.

The acquisition process of musical tonal schema: implications from connectionist modeling

PubMed Central

Matsunaga, Rie; Hartono, Pitoyo; Abe, Jun-ichi

2015-01-01

Using connectionist modeling, we address fundamental questions concerning the acquisition process of musical tonal schema of listeners. Compared to models of previous studies, our connectionist model (Learning Network for Tonal Schema, LeNTS) was better equipped to fulfill three basic requirements. Specifically, LeNTS was equipped with a learning mechanism, bound by culture-general properties, and trained by sufficient melody materials. When exposed to Western music, LeNTS acquired musical ‘scale’ sensitivity early and ‘harmony’ sensitivity later. The order of acquisition of scale and harmony sensitivities shown by LeNTS was consistent with the culture-specific acquisition order shown by musically westernized children. The implications of these results for the acquisition process of a tonal schema of listeners are as follows: (a) the acquisition process may entail small and incremental changes, rather than large and stage-like changes, in corresponding neural circuits; (b) the speed of schema acquisition may mainly depend on musical experiences rather than maturation; and (c) the learning principles of schema acquisition may be culturally invariant while the acquired tonal schemas are varied with exposed culture-specific music. PMID:26441725

Combining Model-driven and Schema-based Program Synthesis

NASA Technical Reports Server (NTRS)

Denney, Ewen; Whittle, John

2004-01-01

We describe ongoing work which aims to extend the schema-based program synthesis paradigm with explicit models. In this context, schemas can be considered as model-to-model transformations. The combination of schemas with explicit models offers a number of advantages, namely, that building synthesis systems becomes much easier since the models can be used in verification and in adaptation of the synthesis systems. We illustrate our approach using an example from signal processing.

Three-dimensional motor schema based navigation

NASA Technical Reports Server (NTRS)

Arkin, Ronald C.

1989-01-01

Reactive schema-based navigation is possible in space domains by extending the methods developed for ground-based navigation found within the Autonomous Robot Architecture (AuRA). Reformulation of two dimensional motor schemas for three dimensional applications is a straightforward process. The manifold advantages of schema-based control persist, including modular development, amenability to distributed processing, and responsiveness to environmental sensing. Simulation results show the feasibility of this methodology for space docking operations in a cluttered work area.

Core schemas and suicidality in a chronically traumatized population.

PubMed

Dutra, Lissa; Callahan, Kelley; Forman, Evan; Mendelsohn, Michaela; Herman, Judith

2008-01-01

The Young Schema Questionnaire (YSQ) has been demonstrated to tap into core beliefs, or maladaptive schemas, of clinical populations. This study used the YSQ to investigate maladaptive schemas of 137 chronically traumatized patients seeking outpatient psychiatric treatment and to assess whether specific schemas might be associated with suicide risk in this population. Participants completed a modified version of the YSQ-S (short form), post-traumatic diagnostic scale, dissociative experiences scale and self-harm and risk behaviors questionnaire-revised at treatment intake. Significant correlations were found between most YSQ scales and the post-traumatic diagnostic scale, and between all YSQ scales and the dissociative experiences scale. Suicide risk variables were most highly correlated with the social isolation/alienation, defectiveness/shame and failure YSQ scales, suggesting that these schemas may mark individuals at particularly high risk for suicidal ideation and suicide attempts. These results offer important implications for the assessment and treatment of high-risk traumatized patients.

Baby schema modulates the brain reward system in nulliparous women.

PubMed

Glocker, Melanie L; Langleben, Daniel D; Ruparel, Kosha; Loughead, James W; Valdez, Jeffrey N; Griffin, Mark D; Sachser, Norbert; Gur, Ruben C

2009-06-02

Ethologist Konrad Lorenz defined the baby schema ("Kindchenschema") as a set of infantile physical features, such as round face and big eyes, that is perceived as cute and motivates caretaking behavior in the human, with the evolutionary function of enhancing offspring survival. The neural basis of this fundamental altruistic instinct is not well understood. Prior studies reported a pattern of brain response to pictures of children, but did not dissociate the brain response to baby schema from the response to children. Using functional magnetic resonance imaging and controlled manipulation of the baby schema in infant faces, we found that baby schema activates the nucleus accumbens, a key structure of the mesocorticolimbic system mediating reward processing and appetitive motivation, in nulliparous women. Our findings suggest that engagement of the mesocorticolimbic system is the neurophysiologic mechanism by which baby schema promotes human caregiving, regardless of kinship.

MedlinePlus Milestones: 1998-present

MedlinePlus

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

ForConX: A forcefield conversion tool based on XML.

PubMed

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

2017-04-05

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

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

NASA Technical Reports Server (NTRS)

Lin, Risheng; Afjeh, Abdollah A.

2003-01-01

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

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

VOTable JAVA Streaming Writer and Applications.

NASA Astrophysics Data System (ADS)

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

2004-07-01

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

Explanation-Based Knowledge Acquisition of Schemas in Practical Electronics: A Machine Learning Approach

DTIC Science & Technology

1990-09-12

electronics reading to the next. To test this hypothesis and the suitability of EBL to acquiring schemas, I have implemented an automated reader/learner as...used. For example, testing the utility of a kidnapping schema using several readings about kidnapping can only go so far toward establishing the...the cost of carrying the new rules while processing unrelated material will be underestimated. The present research tests the utility of new schemas in

The Activation of Incompetence Schemas in Response to Negative Sexual Events in Heterosexual and Lesbian Women: The Moderator Role of Personality Traits and Dysfunctional Sexual Beliefs.

PubMed

Peixoto, Maria Manuela; Nobre, Pedro

2017-01-01

Personality traits and dysfunctional sexual beliefs have been described as vulnerability factors for sexual dysfunction in women, and have also been proposed as dispositional variables for the activation of incompetence schemas in response to negative sexual events. However, no study has tested the role of personality traits and dysfunctional sexual beliefs in the activation of incompetence schemas. The current study aimed to assess the moderator role of neuroticism, extraversion, and dysfunctional sexual beliefs in the association between frequency of unsuccessful sexual episodes and activation of incompetence schemas in heterosexual and lesbian women. An online survey was completed by 1,121 women (831 heterosexual; 290 lesbian). Participants completed the NEO Five-Factor Inventory (NEO-FFI), the Sexual Dysfunctional Beliefs Questionnaire-Female Version (SDBQ), and the Questionnaire of Cognitive Schemas Activated in Sexual Context (QCSASC). Findings indicate that neuroticism moderates the association between frequency of negative sexual events and activation of incompetence schemas in heterosexual women. Moreover, several sexual beliefs also act as moderators of the relationship between negative sexual episodes and the activation of cognitive schemas in both heterosexual and lesbian women. Overall, findings support the cognitive-emotional model of sexual dysfunctions, emphasizing the role of personality traits and dysfunctional sexual beliefs as facilitators of the activation of incompetence schemas in response to negative events in women.

Exploring correlation between perceived parenting styles, early maladaptive schemas, and depression among women with depressive symptoms in iran and India- role of early maladaptive schemas as mediators and moderatos.

PubMed

Khajouei Nia, Maryam; Sovani, Anuradha; Sarami Forooshani, Gholam Reza

2014-12-01

Many studies have reported that inadequate parental styles can contribute to depressive symptoms through dysfunctional cognitive styles. This study aimed to investigate the association of dysfunctional schemas and parenting style with depression, as well as the role of maladaptive schemas such as moderators and mediators in Iran and India. The study sample was selected randomly and consisted of 200 (age group 16-60 y) depressed females (mild to moderate); 100 from Tehran (Iran) and another 100 from Pune (India). The type of the research was causal-comparative. The data collection took place in hospitals and clinics in the targeted cities. Descriptive statistic tests and hierarchical multiple regression were executed (for the purpose of analyzing data) by SPSS 17. It was demonstrated that the association between parenting and depression was not moderated by early maladaptive schemas. On the contrary, the results supported meditational models in which parenting styles are associated with the cognitive schemas, and these in turn are related to depressive symptoms. It was also found that abandonment mediates the impacts of maternal style on depression in Iran. On the other hand, abandonment and punitiveness schemas mediated the relation between paternal style and depression in India. These findings suggest that the correlation between childhood experiences and depression in adulthood are mediated by dysfunctional schemas.

Inpatient schema therapy for nonresponsive patients with personality pathology: Changes in symptomatic distress, schemas, schema modes, coping styles, experienced parenting styles, and mental well-being.

PubMed

Schaap, Grietje M; Chakhssi, Farid; Westerhof, Gerben J

2016-12-01

This study provides an evaluation of group schema therapy (ST) for inpatient treatment of patients with personality pathology who did not respond to previous psychotherapeutic interventions. Forty-two patients were assessed pre- and posttreatment, and 35 patients were evaluated at follow-up 6 months later. The results showed a dropout rate of 35%. Those who dropped out did not differ from those who completed treatment with regard to demographic and clinical variables; the only exception was that those who dropped out showed a lower prevalence of mood disorders. Furthermore, intention-to-treat analyses showed a significant improvement in maladaptive schemas, schema modes, maladaptive coping styles, mental well-being, and psychological distress after treatment, and these improvements were maintained at follow-up. On the other hand, there was no significant change in experienced parenting style as self-reported by patients. Changes in schemas and schema modes measured from pre- to posttreatment were predictive of general psychological distress at follow-up. Overall, these preliminary findings suggest that positive treatment results can be obtained with group ST-based inpatient treatment for patients who did not respond to previous psychotherapeutic interventions. Moreover, these findings are comparable with treatment results for patients without such a nonresponsive treatment history. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

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.

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.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

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

Tongue Scrapers Only Slightly Reduce Bad Breath

MedlinePlus

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

The Role of Ontologies in Schema-based Program Synthesis

NASA Technical Reports Server (NTRS)

Bures, Tomas; Denney, Ewen; Fischer, Bernd; Nistor, Eugen C.

2004-01-01

Program synthesis is the process of automatically deriving executable code from (non-executable) high-level specifications. It is more flexible and powerful than conventional code generation techniques that simply translate algorithmic specifications into lower-level code or only create code skeletons from structural specifications (such as UML class diagrams). Key to building a successful synthesis system is specializing to an appropriate application domain. The AUTOBAYES and AUTOFILTER systems, under development at NASA Ames, operate in the two domains of data analysis and state estimation, respectively. The central concept of both systems is the schema, a representation of reusable computational knowledge. This can take various forms, including high-level algorithm templates, code optimizations, datatype refinements, or architectural information. A schema also contains applicability conditions that are used to determine when it can be applied safely. These conditions can refer to the initial specification, to intermediate results, or to elements of the partially-instantiated code. Schema-based synthesis uses AI technology to recursively apply schemas to gradually refine a specification into executable code. This process proceeds in two main phases. A front-end gradually transforms the problem specification into a program represented in an abstract intermediate code. A backend then compiles this further down into a concrete target programming language of choice. A core engine applies schemas on the initial problem specification, then uses the output of those schemas as the input for other schemas, until the full implementation is generated. Since there might be different schemas that implement different solutions to the same problem this process can generate an entire solution tree. AUTOBAYES and AUTOFILTER have reached the level of maturity where they enable users to solve interesting application problems, e.g., the analysis of Hubble Space Telescope images. They are large (in total around 100kLoC Prolog), knowledge intensive systems that employ complex symbolic reasoning to generate a wide range of non-trivial programs for complex application do- mains. Their schemas can have complex interactions, which make it hard to change them in isolation or even understand what an existing schema actually does. Adding more capabilities by increasing the number of schemas will only worsen this situation, ultimately leading to the entropy death of the synthesis system. The root came of this problem is that the domain knowledge is scattered throughout the entire system and only represented implicitly in the schema implementations. In our current work, we are addressing this problem by making explicit the knowledge from Merent parts of the synthesis system. Here; we discuss how Gruber's definition of an ontology as an explicit specification of a conceptualization matches our efforts in identifying and explicating the domain-specific concepts. We outline the dual role ontologies play in schema-based synthesis and argue that they address different audiences and serve different purposes. Their first role is descriptive: they serve as explicit documentation, and help to understand the internal structure of the system. Their second role is prescriptive: they provide the formal basis against which the other parts of the system (e.g., schemas) can be checked. Their final role is referential: ontologies also provide semantically meaningful "hooks" which allow schemas and tools to access the internal state of the program derivation process (e.g., fragments of the generated code) in domain-specific rather than language-specific terms, and thus to modify it in a controlled fashion. For discussion purposes we use AUTOLINEAR, a small synthesis system we are currently experimenting with, which can generate code for solving a system of linear equations, Az = b.

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

PubMed

Mungall, Christopher J; Emmert, David B

2007-07-01

A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).

Issues and prospects for the next generation of the spatial data transfer standard (SDTS)

USGS Publications Warehouse

Arctur, D.; Hair, D.; Timson, G.; Martin, E.P.; Fegeas, R.

1998-01-01

The Spatial Data Transfer Standard (SDTS) was designed to be capable of representing virtually any data model, rather than being a prescription for a single data model. It has fallen short of this ambitious goal for a number of reasons, which this paper investigates. In addition to issues that might have been anticipated in its design, a number of new issues have arisen since its initial development. These include the need to support explicit feature definitions, incremental update, value-added extensions, and change tracking within large, national databases. It is time to consider the next stage of evolution for SDTS. This paper suggests development of an Object Profile for SDTS that would integrate concepts for a dynamic schema structure, OpenGIS interface, and CORBA IDL.

Positive schemas, psychopathology, and quality of life in children with pediatric cancer: A pilot study.

PubMed

McArthur, Brae Anne; Strother, Douglas; Schulte, Fiona

2017-01-01

Research in the area of pediatric oncology has shown that although some children and youth diagnosed with this disease cope adaptively after their diagnosis, others continue to have long-term psychosocial difficulties. The potential mechanisms that may protect against the experience of psychopathology and poor quality of life within this population are not well known. The purpose of this pilot study was to utilize a new comprehensive measure of positive schemas to better understand the relationship between positive schemas, quality of life, and psychopathology, for children on active treatment for cancer. Participants were 22 patients, aged 8-18 years, being treated in a pediatric oncology clinic. Patients and parents completed measures of positive schemas, quality of life, and psychopathology. The mean age at time of initial diagnosis of the patient sample was 11.6 years. Child-reported positive schemas were significantly related to child-reported child quality of life (r = 0.46, p = 0.03). This is the first study to examine positive schemas within a pediatric oncology sample. Future research is needed to further explore facets of positive schemas that may be particularly relevant to child psychological functioning in a pediatric oncology population.

Early Maladaptive Schemas in a Sample of Airline Pilots seeking Residential Substance Use Treatment: An Initial Investigation

PubMed Central

Shorey, Ryan C.; Brasfield, Hope; Anderson, Scott; Stuart, Gregory L.

2014-01-01

Background Recent research has begun to examine the early maladaptive schemas of substance abusers, as it is believed that targeting these core beliefs in treatment may result in improved substance use outcomes. One special population that has received scant attention in the research literature, despite high levels of substance use, is airline pilots. Aims The current study examined the early maladaptive schemas of a sample of airline pilots (n = 64) who were seeking residential treatment for alcohol dependence and whether they differed in early maladaptive schemas from non-pilot substance abusers who were also seeking residential treatment for alcohol dependence (n = 45). Method Pre-existing medical records from patients of a residential substance abuse treatment facility were reviewed for the current study. Results Of the 18 early maladaptive schemas, results demonstrated that pilots scored higher than non-pilots on the early maladaptive schema of unrelenting standards (high internalized standards of behavior), whereas non-pilots scored higher on insufficient self-control (low frustration tolerance and self-control). Conclusions Early maladaptive schemas may be a relevant treatment target for substance abuse treatment seeking pilots and non-pilots. PMID:24701252

Group Schema Therapy for Eating Disorders: A Pilot Study

PubMed Central

Simpson, Susan G.; Morrow, Emma; van Vreeswijk, Michiel; Reid, Caroline

2010-01-01

This paper describes the use of Group Schema Therapy for Eating Disorders (ST-E-g) in a case series of eight participants with chronic eating disorders and high levels of co-morbidity. Treatment was comprised of 20 sessions which included cognitive, experiential, and interpersonal strategies, with an emphasis on behavioral change. Specific schema-based strategies focused on bodily felt-sense and body-image, as well as emotional regulation skills. Six attended until end of treatment, two dropped-out at mid-treatment. Eating disorder severity, global schema severity, shame, and anxiety levels were reduced between pre- and post-therapy, with a large effect size at follow-up. Clinically significant improvement in eating severity was found in four out of six completers. Group completers showed a mean reduction in schema severity of 43% at post-treatment, and 59% at follow-up. By follow-up, all completers had achieved over 60% improvement in schema severity. Self-report feedback suggests that group factors may catalyze the change process in schema therapy by increasing perceptions of support and encouragement to take risks and try out new behaviors, whilst providing a de-stigmatizing and de-shaming therapeutic experience. PMID:21833243

Early maladaptive schemas and suicidal risk in an Iranian sample of patients with obsessive-compulsive disorder.

PubMed

Khosravani, Vahid; Sharifi Bastan, Farangis; Samimi Ardestani, Mehdi; Jamaati Ardakani, Razieh

2017-09-01

There are few studies on suicidal risk and its related factors in patients diagnosed with obsessive-compulsive disorder (OCD). This study investigated the associations of early maladaptive schemas, OC symptom dimensions, OCD severity, depression and anxiety with suicidality (i.e., suicidal ideation and suicide attempts) in OCD patients. Sixty OCD outpatients completed the Scale for Suicide Ideation (SSI), the Young Schema Questionnaire-Short Form (YSQ-SF), the Yale-Brown Obsessive Compulsive Scale (Y-BOCS), the Dimensional Obsessive-Compulsive Scale (DOCS) and the Depression Anxiety Stress Scales (DASS-21). 51.7% of patients had lifetime suicide attempts and 75% had suicidal ideation. OCD patients with lifetime suicide attempts exhibited significantly higher scores on early maladaptive schemas than those without such attempts. Logistic regression analysis revealed that the mistrust/abuse schema and the OC symptom dimension of unacceptable thoughts explained lifetime suicide attempts. The mistrust/abuse schema, unacceptable thoughts and depression significantly predicted suicidal ideation. These findings indicated that the mistrust/abuse schema may contribute to high suicidality in OCD patients. Also, patients suffering from unacceptable thoughts need to be assessed more carefully for warning signs of suicide. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

True and false recall and dissociation among maltreated children: the role of self-schema.

PubMed

Valentino, Kristin; Cicchetti, Dante; Rogosch, Fred A; Toth, Sheree L

2008-01-01

The current investigation addresses the manner through which trauma affects basic memory and self-system processes. True and false recall for self-referent stimuli were assessed in conjunction with dissociative symptomatology among abused (N=76), neglected (N=92), and nonmaltreated (N=116) school-aged children. Abused, neglected, and nonmaltreated children did not differ in the level of processing self-schema effect or in the occurrence and frequency of false recall. Rather, differences in the affective valence of false recall emerged as a function of maltreatment subtype and age. Regarding dissociation, the abused children displayed higher levels of dissociative symptomatology than did the nonmaltreated children. Although abused, neglected, and nonmaltreated children did not exhibit differences in the valence of their self-schemas, positive and negative self-schemas were related to self-integration differently among the subgroups of maltreatment. Negative self-schemas were associated with increased dissociation among the abused children, whereas positive self-schemas were related to increased dissociation for the neglected children. Thus, positive self-schemas displayed by the younger neglected children were related to higher dissociation, suggestive of defensive self-processing. Implications for clinical intervention are underscored.

Continued Bullying Victimization in Adolescents: Maladaptive Schemas as a Mediational Mechanism.

PubMed

Calvete, Esther; Fernández-González, Liria; González-Cabrera, Joaquín M; Gámez-Guadix, Manuel

2018-03-01

Bullying victimization in adolescence is a significant social problem that can become persistent over time for some victims. However, there is an overall paucity of research examining the factors that contribute to continued bullying victimization. Schema therapy proposes a model that can help us understand why bullying victimization can be persistent for some victims. This study examines the role of maladaptive schemas, the key concept in schema therapy, as a mechanism of continued bullying victimization. The hypothesis was that maladaptive schemas of rejection mediate the predictive association between victimization in both the family and at school and future bullying victimization. Social anxiety was also considered, as previous research suggests that it can increase the risk of victimization. The participants were 1328 adolescents (45% female) with a mean age of 15.05 years (SD = 1.37), who completed questionnaires at three time points with a 6-month interval between them. Time 2 maladaptive schemas of rejection significantly mediated the predictive association from Time 1 bullying victimization, family abuse and social anxiety to Time 3 bullying victimization. The findings pertaining to potentially malleable factors, such as maladaptive schemas that maintain continued interpersonal victimization, have important implications for prevention and treatment strategies with adolescents.

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.

Schema Versioning for Multitemporal Relational Databases.

ERIC Educational Resources Information Center

De Castro, Cristina; Grandi, Fabio; Scalas, Maria Rita

1997-01-01

Investigates new design options for extended schema versioning support for multitemporal relational databases. Discusses the improved functionalities they may provide. Outlines options and basic motivations for the new design solutions, as well as techniques for the management of proposed schema versioning solutions, includes algorithms and…

Improving Listening Comprehension through a Whole-Schema Approach.

ERIC Educational Resources Information Center

Ellermeyer, Deborah

1993-01-01

Examines the development of the schema, or cognitive structure, theory of reading comprehension. Advances a model for improving listening comprehension within the classroom through a teacher-facilitated approach which leads students to selecting and utilizing existing schema within a whole-language environment. (MDM)

The XML Metadata Editor of GFZ Data Services

NASA Astrophysics Data System (ADS)

Ulbricht, Damian; Elger, Kirsten; Tesei, Telemaco; Trippanera, Daniele

2017-04-01

Following the FAIR data principles, research data should be Findable, Accessible, Interoperable and Reuseable. Publishing data under these principles requires to assign persistent identifiers to the data and to generate rich machine-actionable metadata. To increase the interoperability, metadata should include shared vocabularies and crosslink the newly published (meta)data and related material. However, structured metadata formats tend to be complex and are not intended to be generated by individual scientists. Software solutions are needed that support scientists in providing metadata describing their data. To facilitate data publication activities of 'GFZ Data Services', we programmed an XML metadata editor that assists scientists to create metadata in different schemata popular in the earth sciences (ISO19115, DIF, DataCite), while being at the same time usable by and understandable for scientists. Emphasis is placed on removing barriers, in particular the editor is publicly available on the internet without registration [1] and the scientists are not requested to provide information that may be generated automatically (e.g. the URL of a specific licence or the contact information of the metadata distributor). Metadata are stored in browser cookies and a copy can be saved to the local hard disk. To improve usability, form fields are translated into the scientific language, e.g. 'creators' of the DataCite schema are called 'authors'. To assist filling in the form, we make use of drop down menus for small vocabulary lists and offer a search facility for large thesauri. Explanations to form fields and definitions of vocabulary terms are provided in pop-up windows and a full documentation is available for download via the help menu. In addition, multiple geospatial references can be entered via an interactive mapping tool, which helps to minimize problems with different conventions to provide latitudes and longitudes. Currently, we are extending the metadata editor to be reused to generate metadata for data discovery and contextual metadata developed by the 'Multi-scale Laboratories' Thematic Core Service of the European Plate Observing System (EPOS-IP). The Editor will be used to build a common repository of a large variety of geological and geophysical datasets produced by multidisciplinary laboratories throughout Europe, thus contributing to a significant step toward the integration and accessibility of earth science data. This presentation will introduce the metadata editor and show the adjustments made for EPOS-IP. [1] http://dataservices.gfz-potsdam.de/panmetaworks/metaedit

Group schema therapy for eating disorders: study protocol.

PubMed

Calvert, Fiona; Smith, Evelyn; Brockman, Rob; Simpson, Susan

2018-01-01

The treatment of eating disorders is a difficult endeavor, with only a relatively small proportion of clients responding to and completing standard cognitive behavioural therapy (CBT). Given the prevalence of co-morbidity and complex personality traits in this population, Schema Therapy has been identified as a potentially viable treatment option. A case series of Group Schema Therapy for Eating Disorders (ST-E-g) yielded positive findings and the study protocol outlined in this article aims to extend upon these preliminary findings to evaluate group Schema Therapy for eating disorders in a larger sample ( n  = 40). Participants undergo a two-hour assessment where they complete a number of standard questionnaires and their diagnostic status is ascertained using the Eating Disorder Examination. Participants then commence treatment, which consists of 25 weekly group sessions lasting for 1.5 h and four individual sessions. Each group consists of five to eight participants and is facilitated by two therapists, at least one of who is a registered psychologist trained on schema therapy. The primary outcome in this study is eating disorder symptom severity. Secondary outcomes include: cognitive schemas, self-objectification, general quality of life, self-compassion, schema mode presentations, and Personality Disorder features. Participants complete psychological measures and questionnaires at pre, post, six-month and 1-year follow-up. This study will expand upon preliminary research into the efficacy of group Schema Therapy for individuals with eating disorders. If group Schema Therapy is shown to reduce eating disorder symptoms, it will hold considerable promise as an intervention option for a group of disorders that is typically difficult to treat. ACTRN12615001323516. Registered: 2/12/2015 (retrospectively registered, still recruiting).

Schemas and memory consolidation.

PubMed

Tse, Dorothy; Langston, Rosamund F; Kakeyama, Masaki; Bethus, Ingrid; Spooner, Patrick A; Wood, Emma R; Witter, Menno P; Morris, Richard G M

2007-04-06

Memory encoding occurs rapidly, but the consolidation of memory in the neocortex has long been held to be a more gradual process. We now report, however, that systems consolidation can occur extremely quickly if an associative "schema" into which new information is incorporated has previously been created. In experiments using a hippocampal-dependent paired-associate task for rats, the memory of flavor-place associations became persistent over time as a putative neocortical schema gradually developed. New traces, trained for only one trial, then became assimilated and rapidly hippocampal-independent. Schemas also played a causal role in the creation of lasting associative memory representations during one-trial learning. The concept of neocortical schemas may unite psychological accounts of knowledge structures with neurobiological theories of systems memory consolidation.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

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

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

Suggestions for Improvement of User Access to GOCE L2 Data

NASA Astrophysics Data System (ADS)

Tscherning, C. C.

2011-07-01

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

An XML-based method for astronomy software designing

NASA Astrophysics Data System (ADS)

Liao, Mingxue; Aili, Yusupu; Zhang, Jin

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

Utilizing the Structure and Content Information for XML Document Clustering

NASA Astrophysics Data System (ADS)

Tran, Tien; Kutty, Sangeetha; Nayak, Richi

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

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.

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.

Integrating some mind and brain views of transference: the phenomena.

PubMed

Levin, F M

1997-01-01

Because understanding the underpinnings of transferential learning allows the analyst to more effectively exploit transference in the clinical situation, as well as to advance psychoanalytic theory, the functions and mechanisms of transference phenomena in learning are subjected to an interdisciplinary analysis. Through transference the brain creates hierarchical databases that make emotional sense of the world, especially the world of human relationships. Transference plays a role in defense and resistance clinically; less explored but equally important is the adaptive potential of transference and its effect on an individual's readiness for structural change through the activation of working memory. Most investigators within psychoanalysis have not considered the importance of similarity judgments and memory priming, especially as these help to explain why transference and its proper handling are effective in treatment. Yet there are complex relationships among transference, similarity judgment, and memory priming that tie together psychoanalysis, cognitive psychology, and neurophysiology. Evidence increasingly suggests a relationship between transference and the transfer of knowledge between various content domains (databases) of mind and brain, which is essential to cognitive and emotional learning. There are indications as well that transference decisively facilitates learning readiness ("windows") in general by means of two of its components: free association and spontaneous (self-initiated) activity. The important question of which mind/brain mechanisms motivate transference is not yet understood comprehensively. However, Vygotsky's work on the zone of proximal development (ZPD), M.Stern's teleonomic theory, schema theory, and neural network theory offer further insights into what motivates transference.

How Do DSM-5 Personality Traits Align With Schema Therapy Constructs?

PubMed

Bach, Bo; Lee, Christopher; Mortensen, Erik Lykke; Simonsen, Erik

2016-08-01

DSM-5 offers an alternative model of personality pathology that includes 25 traits. Although personality disorders are mostly treated with psychotherapy, the correspondence between DSM-5 traits and concepts in evidence-based psychotherapy has not yet been evaluated adequately. Suitably, schema therapy was developed for treating personality disorders, and it has achieved promising evidence. The authors examined associations between DSM-5 traits and schema therapy constructs in a mixed sample of 662 adults, including 312 clinical participants. Associations were investigated in terms of factor loadings and regression coefficients in relation to five domains, followed by specific correlations among all constructs. The results indicated conceptually coherent associations, and 15 of 25 traits were strongly related to relevant schema therapy constructs. Conclusively, DSM-5 traits may be considered expressions of schema therapy constructs, which psychotherapists might take advantage of in terms of case formulation and targets of treatment. In turn, schema therapy constructs add theoretical understanding to DSM-5 traits.

Early maladaptive schemas in personality disordered individuals.

PubMed

Jovev, Martina; Jackson, Henry J

2004-10-01

The present study aimed to examine the specificity of schema domains in three personality disorder (PD) groups, namely borderline (BPD), obsessive-compulsive (OCPD), and avoidant PD (AvPD), and to correctly identify the three PD groups on the basis of these schemas. The sample consisted of 48 clinical participants diagnosed with PDs and assigned to 1 of 3 groups on the basis of their Axis II diagnoses (BPD: n = 13; OCPD: n = 13; AvPD: n = 22). High scores on Dependence/Incompetence, Defectiveness/ Shame and Abandonment were found for the BPD group. Such pattern appears to be most consistent with Young's theory of BPD. Consistent with the theory and empirical findings of Beck et al. (1990, 2001), OCPD was associated with elevations on the Unrelenting Standards schema domain, but not on Emotional Inhibition, which was found to be elevated for AvPD. In conclusion, the present study suggests that there are different patterns of schema domains across different PDs and that the Schema Questionnaire (SQ) is potentially useful in differentiating between these PDs.

Topological Schemas of Cognitive Maps and Spatial Learning.

PubMed

Babichev, Andrey; Cheng, Sen; Dabaghian, Yuri A

2016-01-01

Spatial navigation in mammals is based on building a mental representation of their environment-a cognitive map. However, both the nature of this cognitive map and its underpinning in neural structures and activity remains vague. A key difficulty is that these maps are collective, emergent phenomena that cannot be reduced to a simple combination of inputs provided by individual neurons. In this paper we suggest computational frameworks for integrating the spiking signals of individual cells into a spatial map, which we call schemas. We provide examples of four schemas defined by different types of topological relations that may be neurophysiologically encoded in the brain and demonstrate that each schema provides its own large-scale characteristics of the environment-the schema integrals. Moreover, we find that, in all cases, these integrals are learned at a rate which is faster than the rate of complete training of neural networks. Thus, the proposed schema framework differentiates between the cognitive aspect of spatial learning and the physiological aspect at the neural network level.

Cognitive structures in women with sexual dysfunction: the role of early maladaptive schemas.

PubMed

Oliveira, Cátia; Nobre, Pedro J

2013-07-01

Cognitive schemas are often related to psychological problems. However, the role of these structures within sexual problems is not yet well established. The aim of this study was to evaluate the presence and importance of early maladaptive schemas on women's sexual functioning and cognitive schemas activated in response to negative sexual events. A total of 228 women participated in the study: a control sample of 167 women without sexual problems, a subclinical sample of 37 women with low sexual functioning, and a clinical sample of 24 women with sexual dysfunction. Participants completed several self-reported measures: the Schema Questionnaire, the Questionnaire of Cognitive Schema Activation in Sexual Context, the Brief Symptom Inventory, the Beck Depression Inventory, and the Female Sexual Function Index. Findings indicated that women with sexual dysfunction presented significantly more early maladaptive schemas from the Impaired Autonomy and Performance domain, particularly failure (P < 0.001, η(2) = 0.08), dependence/incompetence (P < 0.05, η(2) = 0.03), and vulnerability to danger (P < 0.05, η(2) = 0.04). Additionally, in response to negative sexual events, women with sexual dysfunction presented significantly higher scores on incompetence (P < 0.001, η(2) = 0.16), self-depreciation (P < 0.01, η(2) = 0.05), and difference/loneliness (P < 0.01, η(2) = 0.05) schemas. Results supported differences between women with and without sexual problems regarding cognitive factors. This may have implications for the knowledge, assessment, and treatment of sexual dysfunction in women. © 2012 International Society for Sexual Medicine.

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.

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.

Testing Three-Item Versions for Seven of Young's Maladaptive Schema

ERIC Educational Resources Information Center

Blau, Gary; DiMino, John; Sheridan, Natalie; Pred, Robert S.; Beverly, Clyde; Chessler, Marcy

2015-01-01

The Young Schema Questionnaire (YSQ) in either long-form (205- item) or short-form (75-item or 90-item) versions has demonstrated its clinical usefulness for assessing early maladaptive schemas. However, even a 75 or 90-item "short form", particularly when combined with other measures, can represent a lengthy…

Schema Theory: A Basis for Domain Integration Design.

ERIC Educational Resources Information Center

Suzuki, Katsuaki

The cognitive and affective domains of learning outcomes--i.e., intellectual skills, verbal information, cognitive strategies, and attitudes--are parts of every schema. Located within an individual schema, these capabilities are interrelated, and acquiring one capability is likely to have an effect on other types of capabilities within the same…

Young Adolescents' Gender-, Ethnicity-, and Popularity-Based Social Schemas of Aggressive Behavior

ERIC Educational Resources Information Center

Clemans, Katherine H.; Graber, Julia A.

2016-01-01

Social schemas can influence the perception and recollection of others' behavior and may create biases in the reporting of social events. This study investigated young adolescents' (N = 317) gender-, ethnicity-, and popularity-based social schemas of overtly and relationally aggressive behavior. Results indicated that participants associated overt…

Beacon- and Schema-Based Method for Recognizing Algorithms from Students' Source Code

ERIC Educational Resources Information Center

Taherkhani, Ahmad; Malmi, Lauri

2013-01-01

In this paper, we present a method for recognizing algorithms from students programming submissions coded in Java. The method is based on the concept of "programming schemas" and "beacons". Schemas are high-level programming knowledge with detailed knowledge abstracted out, and beacons are statements that imply specific…

Parenting Schemas and the Process of Change

ERIC Educational Resources Information Center

Azar, Sandra T.; Nix, Robert L.; Makin-Byrd, Kerry N.

2005-01-01

Parents' childrearing behaviors are guided by schemas of the caregiving role, their functioning in that role, what children need in general, and what their own children are like in particular. Sometimes, however, parenting schemas can be maladaptive because they are too rigid or simple, involve inappropriate content, or are dominated by negative…

Understanding Schemas and Emotion in Early Childhood

ERIC Educational Resources Information Center

Arnold, Cath

2010-01-01

This book makes explicit connections between young children's spontaneous repeated actions and their representations of their emotional worlds. Drawing on the literature on schemas, attachment theory and family contexts, the author takes schema theory into the territory of the emotions, making it relevant to the social and emotional development…

Thinking Children: Learning about Schemas.

ERIC Educational Resources Information Center

Meade, Anne; Cubey, Pam

Schemas are cognitive structures or forms of thought, like pieces of ideas or concepts. Patterns in children's behavior, or in their drawings and paintings, indicate common themes or threads (schemas) running through them. The action research study described in this report examined the effects on children's learning of intervening in their…

The Potential Role of Conflict Resolution Schemas in Adolescent Psychosocial Adjustment

ERIC Educational Resources Information Center

Jutengren, Goran; Palmerus, Kerstin

2007-01-01

Four specific schemas of cognitive structures that adolescents may hold concerning interpersonal disagreements with their parents were identified, each reflecting an authoritative, authoritarian, indulgent, or a neglecting parenting style. To examine the occurrence of such schemas across high and low levels of psychosocial adjustment, 120 Swedish…

Androgyny Versus Gender Schema: A Comment on Bem's Gender Schema Theory.

ERIC Educational Resources Information Center

Spence, Janet T.; Helmreich, Robert L.

1981-01-01

A logical contradiction in Bem's (1981) theory is outlined. The Bem Sex Role Inventory cannot measure a unidimensional construct, gender schema, and two independent constructs--masculinity and femininity. Such instruments measure self-images of instrumental and expressive personality traits which show little relationship to the constructs…

Family Functioning and Maladaptive Schemas: The Moderating Effects of Optimism

ERIC Educational Resources Information Center

Buri, John R.; Gunty, Amy L.

2008-01-01

Authoritarian parenting is often shown to be associated with negative outcomes for children, including the development of maladaptive schemas. However, this is not the case for all children who experience Authoritarian parenting. Optimism is examined as a moderator in the relationship between Authoritarian parenting and maladaptive schemas that…

Anterior Cingulate Cortex in Schema Assimilation and Expression

ERIC Educational Resources Information Center

Wang, Szu-Han; Tse, Dorothy; Morris, Richard G. M.

2012-01-01

In humans and in animals, mental schemas can store information within an associative framework that enables rapid and efficient assimilation of new information. Using a hippocampal-dependent paired-associate task, we now report that the anterior cingulate cortex is part of a neocortical network of schema storage with NMDA receptor-mediated…

The effects of gender role orientation on team schema: a multivariate analysis of indicators in a US Federal health care organization.

PubMed

Scherer, R F; Petrick, J A

2001-02-01

In this empirical study of 649 employees at a federally supported health care facility in the United States, the authors investigated the effects of individual gender role orientation on team schema. The results indicated (a) that nontraditional male and female employees perceived the greatest amount of group cohesion in their team schemas and (b) that both traditional and nontraditional male employees perceived greater problem-solving potential in their team schemas. Meaningful implications for team composition are discussed.

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

North, Michael J.

SchemaOnRead provides tools for implementing schema-on-read including a single function call (e.g., schemaOnRead("filename")) that reads text (TXT), comma separated value (CSV), raster image (BMP, PNG, GIF, TIFF, and JPG), R data (RDS), HDF5, NetCDF, spreadsheet (XLS, XLSX, ODS, and DIF), Weka Attribute-Relation File Format (ARFF), Epi Info (REC), Pajek network (PAJ), R network (NET), Hypertext Markup Language (HTML), SPSS (SAV), Systat (SYS), and Stata (DTA) files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.

Maladaptive dependency schemas, posttraumatic stress hyperarousal symptoms, and intimate partner aggression perpetration.

PubMed

Kachadourian, Lorig K; Taft, Casey T; Holowka, Darren W; Woodward, Halley; Marx, Brian P; Burns, Anthony

2013-10-01

This study examined the associations between maladaptive dependency-related schemas, posttraumatic stress disorder (PTSD) hyperarousal symptoms, and intimate-partner psychological and physical aggression in a sample of court-referred men (N = 174) participating in a domestic-abuser-intervention program. The men were largely African American; average age was 33.5 years. The extent to which hyperarousal symptoms moderated the association between dependency schemas and aggression was also examined. Maladaptive dependency-related schemas were positively associated with severe psychological, and mild and severe physical aggression perpetration. Hyperarousal symptoms were positively associated with mild and severe psychological aggression, and mild physical aggression perpetration. Multiple regression analyses showed a significant interaction for mild physical aggression: For those with high levels of hyperarousal symptoms, greater endorsement of maladaptive dependency schemas was associated with the perpetration of aggression (B = 0.98, p = .001). For those with low levels of hyperarousal symptoms, there was no association between dependency schemas and aggression (B = 0.04, ns). These findings suggest that focusing on problematic dependency and PTSD-hyperarousal symptoms in domestic-abuser-intervention programs may be helpful, and that examining related variables as possible moderators between dependency schemas and intimate aggression would be a fruitful area for future research. Published 2013. This article is a US Government work and is in the public domain in the USA.

Is `Learning' Science Enough? - A Cultural Model of Religious Students of Science in an Australian Government School

NASA Astrophysics Data System (ADS)

Ferguson, Joseph Paul; Kameniar, Barbara

2014-10-01

This paper investigates the cognitive experiences of four religious students studying evolutionary biology in an inner city government secondary school in Melbourne, Australia. The participants in the study were identified using the Religious Background and Behaviours questionnaire (Connors, Tonigan, & Miller, 1996). Participants were interviewed and asked to respond to questions about their cognitive experiences of studying evolutionary biology. Students' responses were analysed using cultural analysis of discourse to construct a cultural model of religious students of science. This cultural model suggests that these students employ a human schema and a non-human schema, which assert that humans are fundamentally different from non-humans in terms of origins and that humans have a transcendental purpose in life. For these students, these maxims seem to be challenged by their belief that evolutionary biology is dictated by metaphysical naturalism. The model suggests that because the existential foundation of these students is challenged, they employ a believing schema to classify their religious explanations and a learning schema to classify evolutionary biology. These schemas are then hierarchically arranged with the learning schema being made subordinate to the believing schema. Importantly, these students are thus able to maintain their existential foundation while fulfilling the requirements of school science. However, the quality of this "learning" is questionable.

Agreement between coding schemas used to identify bleeding-related hospitalizations in claims analyses of nonvalvular atrial fibrillation patients.

PubMed

Coleman, Craig I; Vaitsiakhovich, Tatsiana; Nguyen, Elaine; Weeda, Erin R; Sood, Nitesh A; Bunz, Thomas J; Schaefer, Bernhard; Meinecke, Anna-Katharina; Eriksson, Daniel

2018-01-01

Schemas to identify bleeding-related hospitalizations in claims data differ in billing codes used and coding positions allowed. We assessed agreement across bleeding-related hospitalization coding schemas for claims analyses of nonvalvular atrial fibrillation (NVAF) patients on oral anticoagulation (OAC). We hypothesized that prior coding schemas used to identify bleeding-related hospitalizations in claim database studies would provide varying levels of agreement in incidence rates. Within MarketScan data, we identified adults, newly started on OAC for NVAF from January 2012 to June 2015. Billing code schemas developed by Cunningham et al., the US Food and Drug Administration (FDA) Mini-Sentinel program, and Yao et al. were used to identify bleeding-related hospitalizations as a surrogate for major bleeding. Bleeds were subcategorized as intracranial hemorrhage (ICH), gastrointestinal (GI), or other. Schema agreement was assessed by comparing incidence, rates of events/100 person-years (PYs), and Cohen's kappa statistic. We identified 151 738 new-users of OAC with NVAF (CHA2DS2-VASc score = 3, [interquartile range = 2-4] and median HAS-BLED score = 3 [interquartile range = 2-3]). The Cunningham, FDA Mini-Sentinel, and Yao schemas identified any bleeding-related hospitalizations in 1.87% (95% confidence interval [CI]: 1.81-1.94), 2.65% (95% CI: 2.57-2.74), and 4.66% (95% CI: 4.55-4.76) of patients (corresponding rates = 3.45, 4.90, and 8.65 events/100 PYs). Kappa agreement across schemas was weak-to-moderate (κ = 0.47-0.66) for any bleeding hospitalization. Near-perfect agreement (κ = 0.99) was observed with the FDA Mini-Sentinel and Yao schemas for ICH-related hospitalizations, but agreement was weak when comparing Cunningham to FDA Mini-Sentinel or Yao (κ = 0.52-0.53). FDA Mini-Sentinel and Yao agreement was moderate (κ = 0.62) for GI bleeding, but agreement was weak when comparing Cunningham to FDA Mini-Sentinel or Yao (κ = 0.44-0.56). For other bleeds, agreement across schemas was minimal (κ = 0.14-0.38). We observed varying levels of agreement among 3 bleeding-related hospitalizations schemas in NVAF patients. © 2018 Wiley Periodicals, Inc.

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 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.

Negative Relational Schemas Predict the Trajectory of Coercive Dynamics During Early Childhood

PubMed Central

Smith, Justin D.; Dishion, Thomas J.; Shaw, Daniel S.; Wilson, Melvin N.

2014-01-01

Coercive family processes are germane to the development of problem behaviors in early childhood, yet the cognitive and affective underpinnings are not well understood. We hypothesized that one antecedent of early coercive interactions is the caregiver’s implicit affective attitudes toward the child, which in this article are termed relational schemas. Relational schemas have previously been linked to coercion and problem behaviors, but there has yet to be an examination of the association between relational schemas and trajectories of coercion during early childhood. We examined 731 indigent caregiver-child dyads (49% female children) from a randomized intervention trial of the Family Check-Up. Predominantly biological mothers participated. A speech sample was used to assess relational schemas at age 2. Coercive interactions were assessed observationally each year between ages 2 and 4. Caregiver and teacher reports of children’s oppositional and aggressive behaviors were collected at age 7.5 and 8.5. Path analysis revealed that negative relational schemas were associated with less steep declines in coercion during this period, which in turn were predictive of ratings of oppositional and aggressive behaviors at age 7.5/8.5 after controlling for baseline levels, positive relational schemas, child gender, ethnicity, and cumulative risk. Intervention condition assignment did not moderate this relationship, suggesting the results represent a naturally occurring process. Given the link between persistent early coercion and later deleterious outcomes, relational schemas that maintain and amplify coercive dynamics represent a potential target for early intervention programs designed to improve parent–child relationships. PMID:25208813

XML: An Introduction.

ERIC Educational Resources Information Center

Lewis, John D.

1998-01-01

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

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

DTIC Science & Technology

2012-04-09

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

Stress Leads to Aberrant Hippocampal Involvement When Processing Schema-Related Information

ERIC Educational Resources Information Center

Vogel, Susanne; Kluen, Lisa Marieke; Fernández, Guillén; Schwabe, Lars

2018-01-01

Prior knowledge, represented as a mental schema, has critical impact on how we organize, interpret, and process incoming information. Recent findings indicate that the use of an existing schema is coordinated by the medial prefrontal cortex (mPFC), communicating with parietal areas. The hippocampus, however, is crucial for encoding…

Social Information Processing as a Mediator between Cognitive Schemas and Aggressive Behavior in Adolescents

ERIC Educational Resources Information Center

Calvete, Esther; Orue, Izaskun

2012-01-01

This longitudinal investigation assessed whether cognitive schemas of justification of violence, mistrust, and narcissism predicted social information processing (SIP), and SIP in turn predicted aggressive behavior in adolescents. A total of 650 adolescents completed measures of cognitive schemas at Time 1, SIP in ambiguous social scenarios at…

Counseling Clients with Chronic Pain: A Religiously Oriented Cognitive Behavior Framework

ERIC Educational Resources Information Center

Robertson, Linda A.; Smith, Heather L.; Ray, Shannon L.; Jones, K. Dayle

2009-01-01

The experience of chronic pain is largely influenced by core schemas and cognitive processes, including those that are religious in nature. When these schemas are negative, they contribute to the exacerbation of pain and related problems. A framework is presented for the identification of problematic religious schemas and their modification…

Individual and Sociocultural Influences on Pre-Adolescent Girls' Appearance Schemas and Body Dissatisfaction

ERIC Educational Resources Information Center

Sinton, Meghan M.; Birch, Leann L.

2006-01-01

Appearance schemas, a suggested cognitive component of body image, have been associated with body dissatisfaction in adolescent and adult samples. This study examined girls' weight status (BMI), depression, and parent, sibling, peer, and media influences as predictors of appearance schemas in 173 pre-adolescent girls. Hierarchical regression…

A Critique of Schema Theory in Reading and a Dual Coding Alternative (Commentary).

ERIC Educational Resources Information Center

Sadoski, Mark; And Others

1991-01-01

Evaluates schema theory and presents dual coding theory as a theoretical alternative. Argues that schema theory is encumbered by lack of a consistent definition, its roots in idealist epistemology, and mixed empirical support. Argues that results of many empirical studies used to demonstrate the existence of schemata are more consistently…

A Natural Teaching Method Based on Learning Theory.

ERIC Educational Resources Information Center

Smilkstein, Rita

1991-01-01

The natural teaching method is active and student-centered, based on schema and constructivist theories, and informed by research in neuroplasticity. A schema is a mental picture or understanding of something we have learned. Humans can have knowledge only to the degree to which they have constructed schemas from learning experiences and practice.…

Ability Related Differences in Schema-Guided Text Processing.

ERIC Educational Resources Information Center

Derry, Sharon J.

A study using a biasing paradigm examined four hypotheses regarding specific mechanisms thought to underlie the Assimilation-plus-Correction (A-C) theory of schema-text interactions. According to this theory, the ideas implied by a schema (type-1 ideas) are thought to be assimilated and obscured, while those ideas representing novel information…

Rape-related cognitive distortions: Preliminary findings on the role of early maladaptive schemas.

PubMed

Sigre-Leirós, Vera; Carvalho, Joana; Nobre, Pedro J

2015-01-01

Despite the important focus on the notion of cognitive distortions in the sexual offending area, the relevance of underlying cognitive schemas in sexual offenders has also been suggested. The aim of the present study was to investigate a potential relationship between Early Maladaptive Schemas (EMSs) and cognitive distortions in rapists. A total of 33 men convicted for rape completed the Bumby Rape Scale (BRS), the Young Schema Questionnaire - Short form-3 (YSQ-S3), the Brief Symptom Inventory (BSI), and the Socially Desirable Response Set Measure (SDRS-5). Results showed a significant relationship between the impaired limits schematic domain and the Justifying Rape dimension of the BRS. Specifically, after controlling for psychological distress levels and social desirability tendency, the entitlement/grandiosity schema from the impaired limits domain was a significant predictor of cognitive distortions related to Justifying Rape themes. Overall, despite preliminary, there is some evidence that the Young's Schema-Focused model namely the impaired limits dimension may contribute for the conceptualization of cognitive distortions in rapists and further investigation is recommended. Copyright © 2015 Elsevier Ltd. All rights reserved.

Do schema processes mediate links between parenting and eating pathology?

PubMed

Sheffield, Alex; Waller, Glenn; Emanuelli, Francesca; Murray, James; Meyer, Caroline

2009-07-01

Adverse parenting experiences are commonly linked to eating pathology. A schema-based model of the development and maintenance of eating pathology proposes that one of the potential mediators of the link between parenting and eating pathology might be the development of schema maintenance processes--mechanisms that operate to help the individual avoid intolerable emotions. To test this hypothesis, 353 female students and 124 female eating-disordered clients were recruited. They completed a measure of perceived parenting experiences as related to schema development (Young Parenting Inventory-Revised (YPI-R)), two measures of schema processes (Young Compensatory Inventory; Young-Rygh Avoidance Inventory (YRAI)) and a measure of eating pathology (Eating Disorders Inventory (EDI)). In support of the hypothesis, certain schema processes did mediate the relationship between specific perceptions of parenting and particular forms of eating pathology, although these were different for the clinical and non-clinical samples. In those patients where parenting is implicated in the development of eating pathology, treatment might need to target the cognitive processes that can explain this link. 2009 John Wiley & Sons, Ltd and Eating Disorders Association

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

Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets

PubMed Central

McKinney, Bill; Meyer, Peter A.; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension—functionality supporting preservation of filesystem structure within Dataverse—which is essential for both in-place computation and supporting non-http data transfers. PMID:27862010

The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction

PubMed Central

2014-01-01

Abstract Building large supertrees involves the collection, storage, and processing of thousands of individual phylogenies to create large phylogenies with thousands to tens of thousands of taxa. Such large phylogenies are useful for macroevolutionary studies, comparative biology and in conservation and biodiversity. No easy to use and fully integrated software package currently exists to carry out this task. Here, we present a new Python-based software package that uses well defined XML schema to manage both data and metadata. It builds on previous versions by 1) including new processing steps, such as Safe Taxonomic Reduction, 2) using a user-friendly GUI that guides the user to complete at least the minimum information required and includes context-sensitive documentation, and 3) a revised storage format that integrates both tree- and meta-data into a single file. These data can then be manipulated according to a well-defined, but flexible, processing pipeline using either the GUI or a command-line based tool. Processing steps include standardising names, deleting or replacing taxa, ensuring adequate taxonomic overlap, ensuring data independence, and safe taxonomic reduction. This software has been successfully used to store and process data consisting of over 1000 trees ready for analyses using standard supertree methods. This software makes large supertree creation a much easier task and provides far greater flexibility for further work. PMID:24891820

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

Lightweight application for generating clinical research information systems: MAGIC.

PubMed

Leskošek, Brane; Pajntar, Marjan

2015-12-01

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

Informal information for web-based engineering catalogues

NASA Astrophysics Data System (ADS)

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

2001-10-01

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

Common Data Model for Neuroscience Data and Data Model Exchange

PubMed Central

Gardner, Daniel; Knuth, Kevin H.; Abato, Michael; Erde, Steven M.; White, Thomas; DeBellis, Robert; Gardner, Esther P.

2001-01-01

Objective: Generalizing the data models underlying two prototype neurophysiology databases, the authors describe and propose the Common Data Model (CDM) as a framework for federating a broad spectrum of disparate neuroscience information resources. Design: Each component of the CDM derives from one of five superclasses—data, site, method, model, and reference—or from relations defined between them. A hierarchic attribute-value scheme for metadata enables interoperability with variable tree depth to serve specific intra- or broad inter-domain queries. To mediate data exchange between disparate systems, the authors propose a set of XML-derived schema for describing not only data sets but data models. These include biophysical description markup language (BDML), which mediates interoperability between data resources by providing a meta-description for the CDM. Results: The set of superclasses potentially spans data needs of contemporary neuroscience. Data elements abstracted from neurophysiology time series and histogram data represent data sets that differ in dimension and concordance. Site elements transcend neurons to describe subcellular compartments, circuits, regions, or slices; non-neuroanatomic sites include sequences to patients. Methods and models are highly domain-dependent. Conclusions: True federation of data resources requires explicit public description, in a metalanguage, of the contents, query methods, data formats, and data models of each data resource. Any data model that can be derived from the defined superclasses is potentially conformant and interoperability can be enabled by recognition of BDML-described compatibilities. Such metadescriptions can buffer technologic changes. PMID:11141510

Misconceived causal explanations for emergent processes.

PubMed

Chi, Michelene T H; Roscoe, Rod D; Slotta, James D; Roy, Marguerite; Chase, Catherine C

2012-01-01

Studies exploring how students learn and understand science processes such as diffusion and natural selection typically find that students provide misconceived explanations of how the patterns of such processes arise (such as why giraffes' necks get longer over generations, or how ink dropped into water appears to "flow"). Instead of explaining the patterns of these processes as emerging from the collective interactions of all the agents (e.g., both the water and the ink molecules), students often explain the pattern as being caused by controlling agents with intentional goals, as well as express a variety of many other misconceived notions. In this article, we provide a hypothesis for what constitutes a misconceived explanation; why misconceived explanations are so prevalent, robust, and resistant to instruction; and offer one approach of how they may be overcome. In particular, we hypothesize that students misunderstand many science processes because they rely on a generalized version of narrative schemas and scripts (referred to here as a Direct-causal Schema) to interpret them. For science processes that are sequential and stage-like, such as cycles of moon, circulation of blood, stages of mitosis, and photosynthesis, a Direct-causal Schema is adequate for correct understanding. However, for science processes that are non-sequential (or emergent), such as diffusion, natural selection, osmosis, and heat flow, using a Direct Schema to understand these processes will lead to robust misconceptions. Instead, a different type of general schema may be required to interpret non-sequential processes, which we refer to as an Emergent-causal Schema. We propose that students lack this Emergent Schema and teaching it to them may help them learn and understand emergent kinds of science processes such as diffusion. Our study found that directly teaching students this Emergent Schema led to increased learning of the process of diffusion. This article presents a fine-grained characterization of each type of Schema, our instructional intervention, the successes we have achieved, and the lessons we have learned. Copyright © 2011 Cognitive Science Society, Inc.

Products and Services Available from the Southern California Earthquake Data Center (SCEDC) and the Southern California Seismic Network (SCSN)

NASA Astrophysics Data System (ADS)

Yu, E.; Bhaskaran, A.; Chen, S.; Chowdhury, F. R.; Meisenhelter, S.; Hutton, K.; Given, D.; Hauksson, E.; Clayton, R. W.

2010-12-01

Currently the SCEDC archives continuous and triggered data from nearly 5000 data channels from 425 SCSN recorded stations, processing and archiving an average of 12,000 earthquakes each year. The SCEDC provides public access to these earthquake parametric and waveform data through its website www.data.scec.org and through client applications such as STP and DHI. This poster will describe the most significant developments at the SCEDC in the past year. Updated hardware: ● The SCEDC has more than doubled its waveform file storage capacity by migrating to 2 TB disks. New data holdings: ● Waveform data: Beginning Jan 1, 2010 the SCEDC began continuously archiving all high-sample-rate strong-motion channels. All seismic channels recorded by SCSN are now continuously archived and available at SCEDC. ● Portable data from El Mayor Cucapah 7.2 sequence: Seismic waveforms from portable stations installed by researchers (contributed by Elizabeth Cochran, Jamie Steidl, and Octavio Lazaro-Mancilla) have been added to the archive and are accessible through STP either as continuous data or associated with events in the SCEDC earthquake catalog. This additional data will help SCSN analysts and researchers improve event locations from the sequence. ● Real time GPS solutions from El Mayor Cucapah 7.2 event: Three component 1Hz seismograms of California Real Time Network (CRTN) GPS stations, from the April 4, 2010, magnitude 7.2 El Mayor-Cucapah earthquake are available in SAC format at the SCEDC. These time series were created by Brendan Crowell, Yehuda Bock, the project PI, and Mindy Squibb at SOPAC using data from the CRTN. The El Mayor-Cucapah earthquake demonstrated definitively the power of real-time high-rate GPS data: they measure dynamic displacements directly, they do not clip and they are also able to detect the permanent (coseismic) surface deformation. ● Triggered data from the Quake Catcher Network (QCN) and Community Seismic Network (CSN): The SCEDC in cooperation with QCN and CSN is exploring ways to archive and distribute data from high density low cost networks. As a starting point the SCEDC will store a dataset from QCN and CSN and distribute it through a separate STP client. New archival methods: ● The SCEDC is exploring the feasibility of archiving and distributing waveform data using cloud computing such as Google Apps. A month of continuous data from the SCEDC archive will be stored in Google Apps and a client developed to access it in a manner similar to STP. XML formats: ● The SCEDC is now distributing earthquake parameter data through web services in QuakeML format. ● The SCEDC in collaboration with the Northern California Earthquake Data Center (NCEDC) and USGS Golden has reviewed and revised the StationXML format to produce version 2.0. The new version includes a rules on extending the schema, use of named complex types, and greater consistency in naming conventions. Based on this work we plan to develop readers and writers of the StationXML format.

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.

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.