Home Page, Sweet Home Page: Creating a Web Presence.

ERIC Educational Resources Information Center

Falcigno, Kathleen; Green, Tim

1995-01-01

Focuses primarily on design issues and practical concerns involved in creating World Wide Web documents for use within an organization. Concerns for those developing Web home pages are: learning HyperText Markup Language (HTML); defining customer group; allocating staff resources for maintenance of documents; providing feedback mechanism for…

Guide to the Internet. The world wide web.

PubMed Central

Pallen, M.

1995-01-01

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals. Images p1554-a Fig 5 PMID:8520402

How to use the WWW to distribute STI

NASA Technical Reports Server (NTRS)

Roper, Donna G.

1994-01-01

This presentation explains how to use the World Wide Web (WWW) to distribute scientific and technical information as hypermedia. WWW clients and servers use the HyperText Transfer Protocol (HTTP) to transfer documents containing links to other text, graphics, video, and sound. The standard language for these documents is the HyperText MarkUp Language (HTML). These are simply text files with formatting codes that contain layout information and hyperlinks. HTML documents can be created with any text editor or with one of the publicly available HTML editors or convertors. HTML can also include links to available image formats. This presentation is available online. The URL is http://sti.larc.nasa. (followed by) gov/demos/workshop/introtext.html.

The New Frontier: Conquering the World Wide Web by Mule.

ERIC Educational Resources Information Center

Gresham, Morgan

1999-01-01

Examines effects of teaching hypertext markup language on students' perceptions of class goals in a networked composition classroom. Suggests sending documents via file transfer protocol by command line and viewing the Web with a textual browser shifted emphasis from writing to coding. Argues that helping students identify a balance between…

Internet Resources: Using Web Pages in Social Studies.

ERIC Educational Resources Information Center

Dale, Jack

1999-01-01

Contends that students in social studies classes can utilize Hypertext Markup Language (HTML) as a presentation and collaborative tool by developing websites. Presents two activities where students submitted webpages for country case studies and created a timeline for the French Revolution. Describes how to use HTML by discussing the various tags.…

So You Wanna Be a Web Author?

ERIC Educational Resources Information Center

Buchanan, Larry

1996-01-01

Defines HyperText Markup Language (HTML) as it relates to the World Wide Web (WWW). Describes steps needed to create HTML files on a UNIX system and to make them accessible via the WWW. Presents a list of basic HTML formatting codes and explains the coding used in the author's personal HTML file. (JMV)

HGML: a hypertext guideline markup language.

PubMed Central

Hagerty, C. G.; Pickens, D.; Kulikowski, C.; Sonnenberg, F.

2000-01-01

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form. PMID:11079898

A comprehensive strategy for designing a Web-based medical curriculum.

PubMed Central

Zucker, J.; Chase, H.; Molholt, P.; Bean, C.; Kahn, R. M.

1996-01-01

In preparing for a full featured online curriculum, it is necessary to develop scaleable strategies for software design that will support the pedagogical goals of the curriculum and which will address the issues of acquisition and updating of materials, of robust content-based linking, and of integration of the online materials into other methods of learning. A complete online curriculum, as distinct from an individual computerized module, must provide dynamic updating of both content and structure and an easy pathway from the professor's notes to the finished online product. At the College of Physicians and Surgeons, we are developing such strategies including a scripted text conversion process that uses the Hypertext Markup Language (HTML) as structural markup rather than as display markup, automated linking by the use of relational databases and the Unified Medical Language System (UMLS), integration of text, images, and multimedia along with interface designs which promote multiple contexts and collaborative study. PMID:8947624

Designing a Virtual Classroom for Distance Learning Students through the Internet.

ERIC Educational Resources Information Center

Bradshaw, Allen

Advantages to using the Internet to deliver instruction include the fact that Hypertext Markup Language (HTML) can be accessed on any computer, broadening the student base to anyone with an Internet browser and a PPP (Point-to-Point Protocol) account. In addition, instructions, lectures, and examples can be linked together for use as students need…

Web-Writing in One Minute--and Beyond.

ERIC Educational Resources Information Center

Hughes, Kenneth

This paper describes how librarians can teach patrons the basics of hypertext markup language (HTML) so that patrons can publish their own homepages on the World Wide Web. With proper use of handouts and practice time afterwards, the three basics of HTML can be conveyed in only 60 seconds. The three basics are: the basic template of Web tags, used…

Online Survey, Enrollment, and Examination: Special Internet Applications in Teacher Education.

ERIC Educational Resources Information Center

Tu, Jho-Ju; Babione, Carolyn; Chen, Hsin-Chu

The Teachers College at Emporia State University in Kansas is now utilizing World Wide Web technology for automating the application procedure for student teaching. The general concepts and some of the key terms that are important for understanding the process involved in this project include: a client-server model, HyperText Markup Language,…

The place of SGML and HTML in building electronic patient records.

PubMed

Pitty, D; Gordon, C; Reeves, P; Capey, A; Vieyra, P; Rickards, T

1997-01-01

The authors are concerned that, although popular, SGML (Standard Generalized Markup Language) is only one approach to capturing, storing, viewing and exchanging healthcare information and does not provide a suitable paradigm for solving most of the problems associated with paper based patient record systems. Although a discussion of the relative merits of SGML, HTML (HyperText Markup Language) may be interesting, we feel such a discussion is avoiding the real issues associated with the most appropriate way to model, represent, and store electronic patient information in order to solve healthcare problems, and therefore the medical informatics community should firstly concern itself with these issues. The paper substantiates this viewpoint and concludes with some suggestions of how progress can be made.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

Benefits and Pitfalls of Using HTML as a CD-ROM Development Tool.

ERIC Educational Resources Information Center

Misanchuk, Earl R.; Schwier, Richard A.

The hypertext markup language (HTML) used to develop pages for the world wide web also has potential for use in creating some types of multimedia instruction destined for CD-ROMs. After providing a brief overview of HTML, this document presents pros and cons relevant to CD-ROM production. HTML can offer compatibility to both Windows and Macintosh…

Development and evaluation of a dynamic web-based application.

PubMed

Hsieh, Yichuan; Brennan, Patricia Flatley

2007-10-11

Traditional consumer health informatics (CHI) applications that were developed for lay public on the Web were commonly written in a Hypertext Markup Language (HTML). As genetics knowledge rapidly advances and requires updating information in a timely fashion, a different content structure is therefore needed to facilitate information delivery. This poster will present the process of developing a dynamic database-driven Web CHI application.

[Radiology information system using HTML, JavaScript, and Web server].

PubMed

Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

1997-12-01

We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

PORIDGE: Postmodern Rhizomatics in Digitally Generated Environments--Do We Need a Metatheory for W3?

ERIC Educational Resources Information Center

Wallmannsberger, Josef

1994-01-01

Discusses the World Wide Web (W3) and its relevance to a philosophy of science. Topics include PORIDGE, an electronically mediated encyclopedia of postmodern knowledge; hypertext mark-up language; W3 as a medium for information ecologies; the relationship between W3 and the user; social manufacture of knowledge; and W3 as a model. (29 references)…

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

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

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.

PubMed

Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

2010-03-03

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.

Catalogue of HI PArameters (CHIPA)

NASA Astrophysics Data System (ADS)

Saponara, J.; Benaglia, P.; Koribalski, B.; Andruchow, I.

2015-08-01

The catalogue of HI parameters of galaxies HI (CHIPA) is the natural continuation of the compilation by M.C. Martin in 1998. CHIPA provides the most important parameters of nearby galaxies derived from observations of the neutral Hydrogen line. The catalogue contains information of 1400 galaxies across the sky and different morphological types. Parameters like the optical diameter of the galaxy, the blue magnitude, the distance, morphological type, HI extension are listed among others. Maps of the HI distribution, velocity and velocity dispersion can also be display for some cases. The main objective of this catalogue is to facilitate the bibliographic queries, through searching in a database accessible from the internet that will be available in 2015 (the website is under construction). The database was built using the open source `` mysql (SQL, Structured Query Language, management system relational database) '', while the website was built with ''HTML (Hypertext Markup Language)'' and ''PHP (Hypertext Preprocessor)''.

Migration of the Three-dimensional Wind Field (3DWF) Model from Linux to Windows and Mobile Platforms

DTIC Science & Technology

2017-11-01

7 Fig. 10 Build executable code ........................................................................... 8 Fig. 11 3DWF GUI’s main web ...can be designed in any Windows operating system with internet access via Microsoft’s Internet Explorer (IE) web browser. For this particular project...Therefore, it is advised to have network security safeguards in place and operate only in a trusted PC. The GUI’s Hypertext Markup Language (HTML) web

Automating Information Assurance for Cyber Situational Awareness within a Smart Cloud System of Systems

DTIC Science & Technology

2014-03-01

Humanitarian Assistance and Disaster Relief HTML HyperText Markup Language IA Information Assurance IAI Israel Aerospace Industries IASA Information ...decision maker at the Command and Control “mini cloud” was of upmost interest . This discussion not only confirmed the need to have information ...2) monitoring for specific cyber attacks on a specified system, (3) alerting information of interest to an operator, and finally (4) allowing the

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.

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.

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping

PubMed Central

2010-01-01

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

PubMed

Pinciroli, Francesco; Masseroli, Marco; Acerbo, Livio A; Bonacina, Stefano; Ferrari, Roberto; Marchente, Mario

2004-01-01

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

Mercury Shopping Cart Interface

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe

2006-01-01

Mercury Shopping Cart Interface (MSCI) is a reusable component of the Power User Interface 5.0 (PUI) program described in another article. MSCI is a means of encapsulating the logic and information needed to describe an orderable item consistent with Mercury Shopping Cart service protocol. Designed to be used with Web-browser software, MSCI generates Hypertext Markup Language (HTML) pages on which ordering information can be entered. MSCI comprises two types of Practical Extraction and Report Language (PERL) modules: template modules and shopping-cart logic modules. Template modules generate HTML pages for entering the required ordering details and enable submission of the order via a Hypertext Transfer Protocol (HTTP) post. Shopping cart modules encapsulate the logic and data needed to describe an individual orderable item to the Mercury Shopping Cart service. These modules evaluate information entered by the user to determine whether it is sufficient for the Shopping Cart service to process the order. Once an order has been passed from MSCI to a deployed Mercury Shopping Cart server, there is no further interaction with the user.

WaterML: an XML Language for Communicating Water Observations Data

NASA Astrophysics Data System (ADS)

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

2007-12-01

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

Home Page: The Mode of Transport through the Information Superhighway

NASA Technical Reports Server (NTRS)

Lujan, Michelle R.

1995-01-01

The purpose of the project with the Aeroacoustics Branch was to create and submit a home page for the internet about branch information. In order to do this, one must also become familiar with the way that the internet operates. Learning HyperText Markup Language (HTML), and the ability to create a document using this language was the final objective in order to place a home page on the internet (World Wide Web). A manual of instructions regarding maintenance of the home page, and how to keep it up to date was also necessary in order to provide branch members with the opportunity to make any pertinent changes.

Geospatial Visualization of Scientific Data Through Keyhole Markup Language

NASA Astrophysics Data System (ADS)

Wernecke, J.; Bailey, J. E.

2008-12-01

The development of virtual globes has provided a fun and innovative tool for exploring the surface of the Earth. However, it has been the paralleling maturation of Keyhole Markup Language (KML) that has created a new medium and perspective through which to visualize scientific datasets. Originally created by Keyhole Inc., and then acquired by Google in 2004, in 2007 KML was given over to the Open Geospatial Consortium (OGC). It became an OGC international standard on 14 April 2008, and has subsequently been adopted by all major geobrowser developers (e.g., Google, Microsoft, ESRI, NASA) and many smaller ones (e.g., Earthbrowser). By making KML a standard at a relatively young stage in its evolution, developers of the language are seeking to avoid the issues that plagued the early World Wide Web and development of Hypertext Markup Language (HTML). The popularity and utility of Google Earth, in particular, has been enhanced by KML features such as the Smithsonian volcano layer and the dynamic weather layers. Through KML, users can view real-time earthquake locations (USGS), view animations of polar sea-ice coverage (NSIDC), or read about the daily activities of chimpanzees (Jane Goodall Institute). Perhaps even more powerful is the fact that any users can create, edit, and share their own KML, with no or relatively little knowledge of manipulating computer code. We present an overview of the best current scientific uses of KML and a guide to how scientists can learn to use KML themselves.

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.

[Development of quality assurance/quality control web system in radiotherapy].

PubMed

Okamoto, Hiroyuki; Mochizuki, Toshihiko; Yokoyama, Kazutoshi; Wakita, Akihisa; Nakamura, Satoshi; Ueki, Heihachi; Shiozawa, Keiko; Sasaki, Koji; Fuse, Masashi; Abe, Yoshihisa; Itami, Jun

2013-12-01

Our purpose is to develop a QA/QC (quality assurance/quality control) web system using a server-side script language such as HTML (HyperText Markup Language) and PHP (Hypertext Preprocessor), which can be useful as a tool to share information about QA/QC in radiotherapy. The system proposed in this study can be easily built in one's own institute, because HTML can be easily handled. There are two desired functions in a QA/QC web system: (i) To review the results of QA/QC for a radiotherapy machine, manuals, and reports necessary for routinely performing radiotherapy through this system. By disclosing the results, transparency can be maintained, (ii) To reveal a protocol for QA/QC in one's own institute using pictures and movies relating to QA/QC for simplicity's sake, which can also be used as an educational tool for junior radiation technologists and medical physicists. By using this system, not only administrators, but also all staff involved in radiotherapy, can obtain information about the conditions and accuracy of treatment machines through the QA/QC web system.

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957

A Platform-Independent Plugin for Navigating Online Radiology Cases.

PubMed

Balkman, Jason D; Awan, Omer A

2016-06-01

Software methods that enable navigation of radiology cases on various digital platforms differ between handheld devices and desktop computers. This has resulted in poor compatibility of online radiology teaching files across mobile smartphones, tablets, and desktop computers. A standardized, platform-independent, or "agnostic" approach for presenting online radiology content was produced in this work by leveraging modern hypertext markup language (HTML) and JavaScript web software technology. We describe the design and evaluation of this software, demonstrate its use across multiple viewing platforms, and make it publicly available as a model for future development efforts.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

Just tell me what you want!: the promise and perils of rapid prototyping with the World Wide Web.

PubMed

Cimino, J J; Socratous, S A

1996-01-01

Construction of applications using the World Wide Web architecture and Hypertext Markup Language (HTML) documents is relatively simple. We are exploring this approach with an application, called PolyMed now in use by surgical residents for one year. We monitored use and obtained user feedback to develop new features and eliminate undesirable ones. The system has been used to keep track of over 4,200 patients. We predicted, several advantages and disadvantages to this approach to prototyping clinical applications. Our experience confirms some advantages (ease of development and customization, ability to exploit non-Web system components, and simplified user interface design) and disadvantages (lack of database management services). Some predicted disadvantages failed to materialize (difficulty modeling a clinical application with hypertext and inconveniences associated with the "connectionless" nature of the Web). We were disappointed to find that while integration of external Web applications (such as Medline) into our application was easy, our users did not find it useful.

Just tell me what you want!: the promise and perils of rapid prototyping with the World Wide Web.

PubMed Central

Cimino, J. J.; Socratous, S. A.

1996-01-01

Construction of applications using the World Wide Web architecture and Hypertext Markup Language (HTML) documents is relatively simple. We are exploring this approach with an application, called PolyMed now in use by surgical residents for one year. We monitored use and obtained user feedback to develop new features and eliminate undesirable ones. The system has been used to keep track of over 4,200 patients. We predicted, several advantages and disadvantages to this approach to prototyping clinical applications. Our experience confirms some advantages (ease of development and customization, ability to exploit non-Web system components, and simplified user interface design) and disadvantages (lack of database management services). Some predicted disadvantages failed to materialize (difficulty modeling a clinical application with hypertext and inconveniences associated with the "connectionless" nature of the Web). We were disappointed to find that while integration of external Web applications (such as Medline) into our application was easy, our users did not find it useful. PMID:8947759

Web-Based Collaborative Publications System: R&Tserve

NASA Technical Reports Server (NTRS)

Abrams, Steve

1997-01-01

R&Tserve is a publications system based on 'commercial, off-the-shelf' (COTS) software that provides a persistent, collaborative workspace for authors and editors to support the entire publication development process from initial submission, through iterative editing in a hierarchical approval structure, and on to 'publication' on the WWW. It requires no specific knowledge of the WWW (beyond basic use) or HyperText Markup Language (HTML). Graphics and URLs are automatically supported. The system includes a transaction archive, a comments utility, help functionality, automated graphics conversion, automated table generation, and an email-based notification system. It may be configured and administered via the WWW and can support publications ranging from single page documents to multiple-volume 'tomes'.

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

Carnes, E.T.; Truett, D.F.; Truett, L.F.

In the handful of years since the World Wide Web (WWW or Web) came into being, Web sites have developed at an astonishing rate. With the influx of Web pages comes a disparity of site types, including personal homepages, commercial sales sites, and educational data. The variety of sites and the deluge of information contained on the Web exemplify the individual nature of the WWW. Whereas some people argue that it is this eclecticism which gives the Web its charm, we propose that sites which are repositories of technical data would benefit from standardization. This paper proffers a methodology formore » publishing ecological research on the Web. The template we describe uses capabilities of HTML (the HyperText Markup Language) to enhance the value of the traditional scientific paper.« less

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

FastScript3D - A Companion to Java 3D

NASA Technical Reports Server (NTRS)

Koenig, Patti

2005-01-01

FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

Development of a Google-based search engine for data mining radiology reports.

PubMed

Erinjeri, Joseph P; Picus, Daniel; Prior, Fred W; Rubin, David A; Koppel, Paul

2009-08-01

The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google's XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like "pneumothorax" yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like "hemangioendothelioma" yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google's interface, radiologists can quickly perform useful searches.

[The therapeutic drug monitoring network server of tacrolimus for Chinese renal transplant patients].

PubMed

Deng, Chen-Hui; Zhang, Guan-Min; Bi, Shan-Shan; Zhou, Tian-Yan; Lu, Wei

2011-07-01

This study is to develop a therapeutic drug monitoring (TDM) network server of tacrolimus for Chinese renal transplant patients, which can facilitate doctor to manage patients' information and provide three levels of predictions. Database management system MySQL was employed to build and manage the database of patients and doctors' information, and hypertext mark-up language (HTML) and Java server pages (JSP) technology were employed to construct network server for database management. Based on the population pharmacokinetic model of tacrolimus for Chinese renal transplant patients, above program languages were used to construct the population prediction and subpopulation prediction modules. Based on Bayesian principle and maximization of the posterior probability function, an objective function was established, and minimized by an optimization algorithm to estimate patient's individual pharmacokinetic parameters. It is proved that the network server has the basic functions for database management and three levels of prediction to aid doctor to optimize the regimen of tacrolimus for Chinese renal transplant patients.

TOPS On-Line: Automating the Construction and Maintenance of HTML Pages

NASA Technical Reports Server (NTRS)

Jones, Kennie H.

1994-01-01

After the Technology Opportunities Showcase (TOPS), in October, 1993, Langley Research Center's (LaRC) Information Systems Division (ISD) accepted the challenge to preserve the investment in information assembled in the TOPS exhibits by establishing a data base. Following the lead of several people at LaRC and others around the world, the HyperText Transport Protocol (HTTP) server and Mosaic were the obvious tools of choice for implementation. Initially, some TOPS exhibitors began the conventional approach of constructing HyperText Markup Language (HTML) pages of their exhibits as input to Mosaic. Considering the number of pages to construct, a better approach was conceived that would automate the construction of pages. This approach allowed completion of the data base construction in a shorter period of time using fewer resources than would have been possible with the conventional approach. It also provided flexibility for the maintenance and enhancement of the data base. Since that time, this approach has been used to automate construction of other HTML data bases. Through these experiences, it is concluded that the most effective use of the HTTP/Mosaic technology will require better tools and techniques for creating, maintaining and managing the HTML pages. The development and use of these tools and techniques are the subject of this document.

Intelligent retrieval of medical images from the Internet

NASA Astrophysics Data System (ADS)

Tang, Yau-Kuo; Chiang, Ted T.

1996-05-01

The object of this study is using Internet resources to provide a cost-effective, user-friendly method to access the medical image archive system and to provide an easy method for the user to identify the images required. This paper describes the prototype system architecture, the implementation, and results. In the study, we prototype the Intelligent Medical Image Retrieval (IMIR) system as a Hypertext Transport Prototype server and provide Hypertext Markup Language forms for user, as an Internet client, using browser to enter image retrieval criteria for review. We are developing the intelligent retrieval engine, with the capability to map the free text search criteria to the standard terminology used for medical image identification. We evaluate retrieved records based on the number of the free text entries matched and their relevance level to the standard terminology. We are in the integration and testing phase. We have collected only a few different types of images for testing and have trained a few phrases to map the free text to the standard medical terminology. Nevertheless, we are able to demonstrate the IMIR's ability to search, retrieve, and review medical images from the archives using general Internet browser. The prototype also uncovered potential problems in performance, security, and accuracy. Additional studies and enhancements will make the system clinically operational.

Hypertext comprehension of deaf and hard-of-hearing students and students with specific language impairment.

PubMed

Blom, Helen; Segers, Eliane; Hermans, Daan; Knoors, Harry; Verhoeven, Ludo

2017-02-01

This paper provides insight into the reading comprehension of hierarchically structured hypertexts within D/HH students and students with SLI. To our knowledge, it is the first study on hypertext comprehension in D/HH students and students with SLI, and it also considers the role of working memory. We compared hypertext versus linear text comprehension in D/HH students and students with SLI versus younger students without language problems who had a similar level of decoding and vocabulary. The results demonstrated no difference in text comprehension between the hierarchically structured hypertext and the linear text. Text comprehension of D/HH students and students with SLI was comparable to that of the students without language problems. In addition, there was a similar positive predictive value of visuospatial and not verbal working memory on hypertext comprehension for all three groups. The findings implicate that educational settings can make use of hierarchically structured hypertexts as well as linear texts and that children can navigate in the digital world from young age on, even if language or working memory problems are present. Copyright © 2016 Elsevier Ltd. All rights reserved.

Client-side Medical Image Colorization in a Collaborative Environment.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2015-01-01

The paper presents an application related to collaborative medicine using a browser based medical visualization system with focus on the medical image colorization process and the underlying open source web development technologies involved. Browser based systems allow physicians to share medical data with their remotely located counterparts or medical students, assisting them during patient diagnosis, treatment monitoring, surgery planning or for educational purposes. This approach brings forth the advantage of ubiquity. The system can be accessed from a any device, in order to process the images, assuring the independence towards having a specific proprietary operating system. The current work starts with processing of DICOM (Digital Imaging and Communications in Medicine) files and ends with the rendering of the resulting bitmap images on a HTML5 (fifth revision of the HyperText Markup Language) canvas element. The application improves the image visualization emphasizing different tissue densities.

Archive of chirp seismic reflection data collected during USGS cruises 00SCC02 and 00SCC04, Barataria Basin, Louisiana, May 12-31 and June 17-July 2, 2000

USGS Publications Warehouse

Calderon, Karynna; Dadisman, S.V.; Kindinger, J.L.; Flocks, J.G.; Wiese, D.S.; Kulp, Mark; Penland, Shea; Britsch, L.D.; Brooks, G.R.

2003-01-01

This archive consists of two-dimensional marine seismic reflection profile data collected in the Barataria Basin of southern Louisiana. These data were acquired in May, June, and July of 2000 aboard the R/V G.K. Gilbert. Included here are data in a variety of formats including binary, American Standard Code for Information Interchange (ASCII), Hyper-Text Markup Language (HTML), shapefiles, and Graphics Interchange Format (GIF) and Joint Photographic Experts Group (JPEG) images. Binary data are in Society of Exploration Geophysicists (SEG) SEG-Y format and may be downloaded for further processing or display. Reference maps and GIF images of the profiles may be viewed with a web browser. The Geographic Information Systems (GIS) information provided here is compatible with Environmental Systems Research Institute (ESRI) GIS software.

Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

NASA Astrophysics Data System (ADS)

Lahti, Paul M.; Motyka, Eric J.; Lancashire, Robert J.

2000-05-01

A straightforward procedure is described to combine computation of molecular vibrational modes using commonly available molecular modeling programs with visualization of the modes using advanced features of the MDL Information Systems Inc. Chime World Wide Web browser plug-in. Minor editing of experimental spectra that are stored in the JCAMP-DX format allows linkage of IR spectral frequency ranges to Chime molecular display windows. The spectra and animation files can be combined by Hypertext Markup Language programming to allow interactive linkage between experimental spectra and computationally generated vibrational displays. Both the spectra and the molecular displays can be interactively manipulated to allow the user maximum control of the objects being viewed. This procedure should be very valuable not only for aiding students through visual linkage of spectra and various vibrational animations, but also by assisting them in learning the advantages and limitations of computational chemistry by comparison to experiment.

Data Display Markup Language (DDML) Handbook

DTIC Science & Technology

2017-01-31

Moreover, the tendency of T&E is towards a plug-and-play-like data acquisition system that requires standard languages and modules for data displays...Telemetry Group DOCUMENT 127-17 DATA DISPLAY MARKUP LANGUAGE (DDML) HANDBOOK DISTRIBUTION A: APPROVED FOR...DOCUMENT 127-17 DATA DISPLAY MARKUP LANGUAGE (DDML) HANDBOOK January 2017 Prepared by Telemetry Group

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

Answer Markup Algorithms for Southeast Asian Languages.

ERIC Educational Resources Information Center

Henry, George M.

1991-01-01

Typical markup methods for providing feedback to foreign language learners are not applicable to languages not written in a strictly linear fashion. A modification of Hart's edit markup software is described, along with a second variation based on a simple edit distance algorithm adapted to a general Southeast Asian font system. (10 references)…

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)

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language.

PubMed

Adams, Nico; Winter, Jerry; Murray-Rust, Peter; Rzepa, Henry S

2008-11-01

Polymers are among the most important classes of materials but are only inadequately supported by modern informatics. The paper discusses the reasons why polymer informatics is considerably more challenging than small molecule informatics and develops a vision for the computer-aided design of polymers, based on modern semantic web technologies. The paper then discusses the development of Polymer Markup Language (PML). PML is an extensible language, designed to support the (structural) representation of polymers and polymer-related information. PML closely interoperates with Chemical Markup Language (CML) and overcomes a number of the previously identified challenges.

XML Style Guide

DTIC Science & Technology

2015-07-01

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

An object-oriented approach for harmonization of multimedia markup languages

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

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.

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.

System to monitor data analyses and results of physics data validation between pulses at DIII-D

NASA Astrophysics Data System (ADS)

Flanagan, S.; Schachter, J. M.; Schissel, D. P.

2004-06-01

A data analysis monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility (http://nssrv1.gat.com:8000/dam). The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded, thus increasing the efficiency of experimental time. An example of a consistency check is comparing the experimentally measured neutron rate and the expected neutron emission, RDD0D. A significant difference between these two values could indicate a problem with one or more diagnostics, or the presence of unanticipated phenomena in the plasma. This system also tracks the progress of MDSplus dispatched data analysis software and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, C Language Integrated Production System to implement expert system logic, and displays its results to multiple web clients via Hypertext Markup Language. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse.

Adobe acrobat: an alternative electronic teaching file construction methodology independent of HTML restrictions.

PubMed

Katzman, G L

2001-03-01

The goal of the project was to create a method by which an in-house digital teaching file could be constructed that was simple, inexpensive, independent of hypertext markup language (HTML) restrictions, and appears identical on multiple platforms. To accomplish this, Microsoft PowerPoint and Adobe Acrobat were used in succession to assemble digital teaching files in the Acrobat portable document file format. They were then verified to appear identically on computers running Windows, Macintosh Operating Systems (OS), and the Silicon Graphics Unix-based OS as either a free-standing file using Acrobat Reader software or from within a browser window using the Acrobat browser plug-in. This latter display method yields a file viewed through a browser window, yet remains independent of underlying HTML restrictions, which may confer an advantage over simple HTML teaching file construction. Thus, a hybrid of HTML-distributed Adobe Acrobat generated WWW documents may be a viable alternative for digital teaching file construction and distribution.

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

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

TMATS/ IHAL/ DDML Schema Validation

DTIC Science & Technology

2017-02-01

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

TELLTALE: Experiments in a Dynamic Hypertext Environment for Degraded and Multilingual Data.

ERIC Educational Resources Information Center

Pearce, Claudia; Nicholas, Charles

1996-01-01

Presents experimentation results for the TELLTALE system, a dynamic hypertext environment that provides full-text search from a hypertext-style user interface for text corpora that may be garbled by OCR (optical character recognition) or transmission errors, and that may contain languages other than English. (Author/LRW)

Trends, Fashions, Patterns, Norms, Conventions...and Hypertext Too.

ERIC Educational Resources Information Center

Amitay, Einat

2001-01-01

Outlines the theory behind the formation of language conventions, then reveals conventions evolving in the community of people writing hypertext on the Web. Demonstrates how these conventions can be used to augment and shift the meaning of already published hypertexts. Describes the system called InCommonSense, which reuses particular hypertext…

TumorML: Concept and requirements of an in silico cancer modelling markup language.

PubMed

Johnson, David; Cooper, Jonathan; McKeever, Steve

2011-01-01

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification.

Hypertext Annotation: Effects of Presentation Formats and Learner Proficiency on Reading Comprehension and Vocabulary Learning in Foreign Languages

ERIC Educational Resources Information Center

Chen, I-Jung; Yen, Jung-Chuan

2013-01-01

This study extends current knowledge by exploring the effect of different annotation formats, namely in-text annotation, glossary annotation, and pop-up annotation, on hypertext reading comprehension in a foreign language and vocabulary acquisition across student proficiencies. User attitudes toward the annotation presentation were also…

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

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

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

PubMed Central

Sailors, R. Matthew

2001-01-01

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

An Investigation of Scaffolded Reading on EFL Hypertext Comprehension

ERIC Educational Resources Information Center

Shang, Hui-Fang

2015-01-01

With the rapid growth of computer technology, some printed texts are designed as hypertexts to help EFL (English as a foreign language) learners search for and process multiple resources in a timely manner for autonomous learning. The purpose of this study was to design a hypertext system and examine if a 14-week teacher-guided print-based and…

XML Based Markup Languages for Specific Domains

NASA Astrophysics Data System (ADS)

Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

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

DDML Schema Validation

DTIC Science & Technology

2016-02-08

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

Improving Interoperability by Incorporating UnitsML Into Markup Languages

PubMed Central

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

2010-01-01

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

Improving Interoperability by Incorporating UnitsML Into Markup Languages.

PubMed

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

2010-01-01

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

Enhancing Web applications in radiology with Java: estimating MR imaging relaxation times.

PubMed

Dagher, A P; Fitzpatrick, M; Flanders, A E; Eng, J

1998-01-01

Java is a relatively new programming language that has been used to develop a World Wide Web-based tool for estimating magnetic resonance (MR) imaging relaxation times, thereby demonstrating how Java may be used for Web-based radiology applications beyond improving the user interface of teaching files. A standard processing algorithm coded with Java is downloaded along with the hypertext markup language (HTML) document. The user (client) selects the desired pulse sequence and inputs data obtained from a region of interest on the MR images. The algorithm is used to modify selected MR imaging parameters in an equation that models the phenomenon being evaluated. MR imaging relaxation times are estimated, and confidence intervals and a P value expressing the accuracy of the final results are calculated. Design features such as simplicity, object-oriented programming, and security restrictions allow Java to expand the capabilities of HTML by offering a more versatile user interface that includes dynamic annotations and graphics. Java also allows the client to perform more sophisticated information processing and computation than is usually associated with Web applications. Java is likely to become a standard programming option, and the development of stand-alone Java applications may become more common as Java is integrated into future versions of computer operating systems.

Asia-Pacific POPIN workshop on Internet.

PubMed

1996-01-01

This brief article announces the accomplishments of the ESCAP Population Division of the Department of Economic and Social Information and Policy Analysis (DESIPA) in conjunction with the Asia-Pacific POPIN Internet (Information Superhighway) Training Workshop in popularizing useful new computer information technologies. A successful workshop was held in Bangkok in November 1996 for 18 people from 8 countries in the Asian and Pacific region, many of whom were from population information centers. Participants were taught some techniques for disseminating population data and information through use of the Internet computer facility. Participants learned 1) how to use Windows software in the ESCAP local area network (LAN), 2) about concepts such as HTML (hypertext mark-up language), and 3) detailed information about computer language. Computer practices involved "surfing the Net (Internet)" and linking with the global POPIN site on the Internet. Participants learned about computer programs for information handling and learned how to prepare documents using HTML, how to mount information on the World Wide Web (WWW) of the Internet, how to convert existing documents into "HTML-style" files, and how to scan graphics, such as logos, photographs, and maps, for visual display on the Internet. The Workshop and the three training modules was funded by the UN Population Fund (UNFPA). The POPIN Coordinator was pleased that competency was accomplished in such a short period of time.

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.

Development of Markup Language for Medical Record Charting: A Charting Language.

PubMed

Jung, Won-Mo; Chae, Younbyoung; Jang, Bo-Hyoung

2015-01-01

Nowadays a lot of trials for collecting electronic medical records (EMRs) exist. However, structuring data format for EMR is an especially labour-intensive task for practitioners. Here we propose a new mark-up language for medical record charting (called Charting Language), which borrows useful properties from programming languages. Thus, with Charting Language, the text data described in dynamic situation can be easily used to extract information.

SGML-Based Markup for Literary Texts: Two Problems and Some Solutions.

ERIC Educational Resources Information Center

Barnard, David; And Others

1988-01-01

Identifies the Standard Generalized Markup Language (SGML) as the best basis for a markup standard for encoding literary texts. Outlines solutions to problems using SGML and discusses the problem of maintaining multiple views of a document. Examines several ways of reducing the burden of markups. (GEA)

Decision Facilitator for Launch Operations using Intelligent Agents

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar; Bardina, Jorge

2005-01-01

Launch operations require millions of micro-decisions which contribute to the macro decision of 'Go/No-Go' for a launch. Knowledge workers"(such as managers and technical professionals) need information in a timely precise manner as it can greatly affect mission success. The intelligent agent (web search agent) uses the words of a hypertext markup language document which is connected through the internet. The intelligent agent's actions are to determine if its goal of seeking a website containing a specified target (e.g., keyword or phrase), has been met. There are few parameters that should be defined for the keyword search like "Go" and "No-Go". Instead of visiting launch and range decision making servers individually, the decision facilitator constantly connects to all servers, accumulating decisions so the final decision can be decided in a timely manner. The facilitator agent uses the singleton design pattern, which ensures that only a single instance of the facilitator agent exists at one time. Negotiations could proceed between many agents resulting in a final decision. This paper describes details of intelligent agents and their interaction to derive an unified decision support system.

Descriptive Metadata: Emerging Standards.

ERIC Educational Resources Information Center

Ahronheim, Judith R.

1998-01-01

Discusses metadata, digital resources, cross-disciplinary activity, and standards. Highlights include Standard Generalized Markup Language (SGML); Extensible Markup Language (XML); Dublin Core; Resource Description Framework (RDF); Text Encoding Initiative (TEI); Encoded Archival Description (EAD); art and cultural-heritage metadata initiatives;…

Intelligent search and retrieval of a large multimedia knowledgebase for the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Clapis, Paul J.; Byers, William S.

1990-01-01

A document-retrieval assistant (DRA) in a microcomputer format is described which incorporates hypertext and natural language capabilities. Hypertext is used to introduce an intelligent search capability, and the natural-language interface permits access to specific data without the use of keywords. The DRA can be used to access and 'browse' the large multimedia database that is composed of project documentation from the HST.

Teaching with a GIS using existing grade 7--12 curricula

NASA Astrophysics Data System (ADS)

Brown, Stephen Castlebury

As Geographic Information Systems (GIS) become less expensive and easier to use, the demand for individuals knowledgeable of this technology increases. Associated with this is the current and future necessity of a public who understands the wide range of technical proficiencies needed for accurate GIS mapping. On a nationwide basis, GIS education in K--12 schools is rare. In the few instances where a school teaches students about these technologies, it is usually led by a single teacher and is not taught on a school-wide basis. This situation exists despite some research indicating that a classroom GIS might enhance the learning of students. Two primary barriers to teacher use and acceptance of a classroom GIS have been identified. First, most teachers lack any training in the use of a GIS. Secondly, there is conflict over focusing upon teaching about the use of a GIS or teaching with a GIS. Beginning in August of 1996 and concluding in August of 1998, nine separate GIS education programs were conducted for a variety of youths and adult educator audiences. Observations of participant's interactions with the GIS program ArcView would lead to the development of a demonstration curriculum and GIS application. To overcome institutional and educational barriers to youth GIS education, a curriculum partly adapted from existing materials and partly created from original materials was developed in Hypertext Markup Language (HTML). A corresponding GIS application was developed to teach about a GIS while instructing with a GIS. The curriculum was distributed for use on CD-ROM and called Georom. The hypertext curriculum provided lessons and exercises that addressed National Science Education Standards and was accessed using an Internet web browser. The curriculum included World Wide Web links to Internet sites with more information about specific topics. Modifications were made to ArcView's Graphical User Interface (GUI) that maintained the general appearance of its standard GUI, but increased its functionality for classroom use. It was observed that the availability and premise of the hypertext curriculum and GIS application increased school administrator acceptance of classroom GIS education. However, the curriculum and GIS application is still not a completely acceptable alternative to quality inservice education on GIS for many teachers.

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…

Symmetric Key Services Markup Language (SKSML)

NASA Astrophysics Data System (ADS)

Noor, Arshad

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

DAVE-ML Utility Programs

NASA Technical Reports Server (NTRS)

Jackson, Bruce

2006-01-01

DAVEtools is a set of Java archives that embodies tools for manipulating flight-dynamics models that have been encoded in dynamic aerospace vehicle exchange markup language (DAVE-ML). [DAVE-ML is an application program, written in Extensible Markup Language (XML), for encoding complete computational models of the dynamics of aircraft and spacecraft.

An Introduction to the Resource Description Framework.

ERIC Educational Resources Information Center

Miller, Eric

1998-01-01

Explains the Resource Description Framework (RDF), an infrastructure developed under the World Wide Web Consortium that enables the encoding, exchange, and reuse of structured metadata. It is an application of Extended Markup Language (XML), which is a subset of Standard Generalized Markup Language (SGML), and helps with expressing semantics.…

Online Metacognitive Strategies, Hypermedia Annotations, and Motivation on Hypertext Comprehension

ERIC Educational Resources Information Center

Shang, Hui-Fang

2016-01-01

This study examined the effect of online metacognitive strategies, hypermedia annotations, and motivation on reading comprehension in a Taiwanese hypertext environment. A path analysis model was proposed based on the assumption that if English as a foreign language learners frequently use online metacognitive strategies and hypermedia annotations,…

Developing a Markup Language for Encoding Graphic Content in Plan Documents

ERIC Educational Resources Information Center

Li, Jinghuan

2009-01-01

While deliberating and making decisions, participants in urban development processes need easy access to the pertinent content scattered among different plans. A Planning Markup Language (PML) has been proposed to represent the underlying structure of plans in an XML-compliant way. However, PML currently covers only textual information and lacks…

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

ERIC Educational Resources Information Center

Chang, May

2000-01-01

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

Evolution of a Structure-Searchable Database into a Prototype for a High-Fidelity SmartPhone App for 62 Common Pesticides Used in Delaware.

PubMed

D'Souza, Malcolm J; Barile, Benjamin; Givens, Aaron F

2015-05-01

Synthetic pesticides are widely used in the modern world for human benefit. They are usually classified according to their intended pest target. In Delaware (DE), approximately 42 percent of the arable land is used for agriculture. In order to manage insectivorous and herbaceous pests (such as insects, weeds, nematodes, and rodents), pesticides are used profusely to biologically control the normal pest's life stage. In this undergraduate project, we first created a usable relational database containing 62 agricultural pesticides that are common in Delaware. Chemically pertinent quantitative and qualitative information was first stored in Bio-Rad's KnowItAll® Informatics System. Next, we extracted the data out of the KnowItAll® system and created additional sections on a Microsoft® Excel spreadsheet detailing pesticide use(s) and safety and handling information. Finally, in an effort to promote good agricultural practices, to increase efficiency in business decisions, and to make pesticide data globally accessible, we developed a mobile application for smartphones that displayed the pesticide database using Appery.io™; a cloud-based HyperText Markup Language (HTML5), jQuery Mobile and Hybrid Mobile app builder.

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.

PubMed

Piccolo, Brian D; Wankhade, Umesh D; Chintapalli, Sree V; Bhattacharyya, Sudeepa; Chunqiao, Luo; Shankar, Kartik

2018-03-15

Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive. DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed. bdpiccolo@uams.edu.

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.

Report of Official Foreign Travel to France May 8-27, 1998

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

mason, j d

1998-06-11

The Department of Energy (DOE) has moved ever more rapidly towards electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Among the most widely adopted standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), which DOE has selected as the basis of its electronic management of documents. Besides the official commitment, which has resulted in several specializedmore » projects, DOE makes heavy use of coding derived from SGML, and its use is likely to increase in the future. Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Microsoft, Adobe, and Netscape, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, I have served since 1985 as Convenor of the international committee responsible for SGML and related standards, ISO/IEC JTC1/WG4 (WG4). During this trip I convened the spring 1998 meeting of WG4 in Paris, France. I also attended a major conference on the use of SGML and XML. At the close of the conference, I chaired a workshop of standards developers looking at ways of improving online searching of electronic documents. Note: Since the end of the meetings in France, JTC1 has raised the level of WG4 to a full Subcommittee; its designator is now ISO/IEC JTC1/SC34. WG4 maintains and continues to enhance several standards. In addition to SGML, which is the basis of HTML and XML, WG4 also works on the Document Style Semantics and Specification Language (DSSSL), which is the basis for the W3C's XSL (eXtensible Style Language, to be used with XML) and the Hypermedia/Time-based Document Structuring Language (HyTime), which is a major influence on the W3C's XLink (XML Linking Language). WG4 is also involved in work with the ISO's TC184, Industrial Data, on the linking of STEP (the standard for the interchange of product model data) with SGML. In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Y-12 Plant. My project team in Information Technology Services has developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at Y-12 and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). Supporting standards development allows DOE and Y-12 both input into the process and the opportunity to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

A Conversion Tool for Mathematical Expressions in Web XML Files.

ERIC Educational Resources Information Center

Ohtake, Nobuyuki; Kanahori, Toshihiro

2003-01-01

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

Extensible Markup Language: How Might It Alter the Software Documentation Process and the Role of the Technical Communicator?

ERIC Educational Resources Information Center

Battalio, John T.

2002-01-01

Describes the influence that Extensible Markup Language (XML) will have on the software documentation process and subsequently on the curricula of advanced undergraduate and master's programs in technical communication. Recommends how curricula of advanced undergraduate and master's programs in technical communication ought to change in order to…

Astronomical Instrumentation System Markup Language

NASA Astrophysics Data System (ADS)

Goldbaum, Jesse M.

2016-05-01

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

Utilizing Internet Technologies in Observatory Control Systems

NASA Astrophysics Data System (ADS)

Cording, Dean

2002-12-01

The 'Internet boom' of the past few years has spurred the development of a number of technologies to provide services such as secure communications, reliable messaging, information publishing and application distribution for commercial applications. Over the same period, a new generation of computer languages have also developed to provide object oriented design and development, improved reliability, and cross platform compatibility. Whilst the business models of the 'dot.com' era proved to be largely unviable, the technologies that they were based upon have survived and have matured to the point were they can now be utilized to build secure, robust and complete observatory control control systems. This paper will describe how Electro Optic Systems has utilized these technologies in the development of its third generation Robotic Observatory Control System (ROCS). ROCS provides an extremely flexible configuration capability within a control system structure to provide truly autonomous robotic observatory operation including observation scheduling. ROCS was built using Internet technologies such as Java, Java Messaging Service (JMS), Lightweight Directory Access Protocol (LDAP), Secure Sockets Layer (SSL), eXtendible Markup Language (XML), Hypertext Transport Protocol (HTTP) and Java WebStart. ROCS was designed to be capable of controlling all aspects of an observatory and be able to be reconfigured to handle changing equipment configurations or user requirements without the need for an expert computer programmer. ROCS consists of many small components, each designed to perform a specific task, with the configuration of the system specified using a simple meta language. The use of small components facilitates testing and makes it possible to prove that the system is correct.

The Effects of Hypertext Gloss on Comprehension and Vocabulary Retention under Incidental and Intentional Learning Conditions

ERIC Educational Resources Information Center

Zandieh, Zeinab; Jafarigohar, Manoochehr

2012-01-01

The present study investigated comprehension, immediate and delayed vocabulary retention under incidental and intentional learning conditions via computer mediated hypertext gloss. One hundred and eighty four (N = 184) intermediate students of English as a foreign language at an English school participated in the study. They were randomly assigned…

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.

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

ERIC Educational Resources Information Center

Walsh, Lucas

2007-01-01

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

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…

Debugging expert systems using a dynamically created hypertext network

NASA Technical Reports Server (NTRS)

Boyle, Craig D. B.; Schuette, John F.

1991-01-01

The labor intensive nature of expert system writing and debugging motivated this study. The hypothesis is that a hypertext based debugging tool is easier and faster than one traditional tool, the graphical execution trace. HESDE (Hypertext Expert System Debugging Environment) uses Hypertext nodes and links to represent the objects and their relationships created during the execution of a rule based expert system. HESDE operates transparently on top of the CLIPS (C Language Integrated Production System) rule based system environment and is used during the knowledge base debugging process. During the execution process HESDE builds an execution trace. Use of facts, rules, and their values are automatically stored in a Hypertext network for each execution cycle. After the execution process, the knowledge engineer may access the Hypertext network and browse the network created. The network may be viewed in terms of rules, facts, and values. An experiment was conducted to compare HESDE with a graphical debugging environment. Subjects were given representative tasks. For speed and accuracy, in eight of the eleven tasks given to subjects, HESDE was significantly better.

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

PubMed

Saadawi, Gilan M; Harrison, James H

2006-10-01

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

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.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

PubMed

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

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.

RTML: remote telescope markup language and you

NASA Astrophysics Data System (ADS)

Hessman, F. V.

2001-12-01

In order to coordinate the use of robotic and remotely operated telescopes in networks -- like Göttingen's MOnitoring NEtwork of Telescopes (MONET) -- a standard format for the exchange of observing requests and reports is needed. I describe the benefits of Remote Telescope Markup Language (RTML), an XML-based protocol originally developed by the Hands-On Universe Project, which is being used and further developed by several robotic telescope projects and firms.

Visualization Development of the Ballistic Threat Geospatial Optimization

DTIC Science & Technology

2015-07-01

topographic globes, Keyhole Markup Language (KML), and Collada files. World Wind gives the user the ability to import 3-D models and navigate...present. After the first person view window is closed , the images stored in memory are then converted to a QuickTime movie (.MOV). The video will be...processing unit HPC high-performance computing JOGL Java implementation of OpenGL KML Keyhole Markup Language NASA National Aeronautics and Space

Experimental Applications of Automatic Test Markup Language (ATML)

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; McCartney, Patrick; Gorringe, Chris

2012-01-01

The authors describe challenging use-cases for Automatic Test Markup Language (ATML), and evaluate solutions. The first case uses ATML Test Results to deliver active features to support test procedure development and test flow, and bridging mixed software development environments. The second case examines adding attributes to Systems Modelling Language (SysML) to create a linkage for deriving information from a model to fill in an ATML document set. Both cases are outside the original concept of operations for ATML but are typical when integrating large heterogeneous systems with modular contributions from multiple disciplines.

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

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

J.D. Mason

2000-07-11

The Department of Energy (DOE) has moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ``standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardization (ISO) and themore » American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, the authors has served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During his June 2000 trip, he chaired the spring 2000 meeting of SC34 in Paris, France. He also attended a major conference on the use of SGML and XML and led a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Oak Ridge Y-12 Plant. The local project team developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The Ferret system for automated classification analysis will use XML to structure its knowledge base. Supporting standards development allows DOE and the Y-12 plant the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

PubMed

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Computer support for physiological cell modelling using an ontology on cell physiology.

PubMed

Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

2006-01-01

The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

NAVAIR Portable Source Initiative (NPSI) Data Preparation Standard V2.2: NPSI DPS V2.2

DTIC Science & Technology

2012-05-22

Keyhole Markup Language (file format) KMZ ............................................................................. Keyhole Markup...required for the geo-specific texture may differ within the database depending on the mission parameters. When operating close to the ground (e.g

Real-time Data Display System of the Korean Neonatal Network

PubMed Central

Lee, Byong Sop; Moon, Wi Hwan

2015-01-01

Real-time data reporting in clinical research networks can provide network members through interim analyses of the registered data, which can facilitate further studies and quality improvement activities. The aim of this report was to describe the building process of the data display system (DDS) of the Korean Neonatal Network (KNN) and its basic structure. After member verification at the KNN member's site, users can choose a variable of interest that is listed in the in-hospital data statistics (for 90 variables) or in the follow-up data statistics (for 54 variables). The statistical results of the outcome variables are displayed on the HyperText Markup Language 5-based chart graphs and tables. Participating hospitals can compare their performance to those of KNN as a whole and identify the trends over time. Ranking of each participating hospital is also displayed in terms of key outcome variables such as mortality and major neonatal morbidities with the names of other centers blinded. The most powerful function of the DDS is the ability to perform 'conditional filtering' which allows users to exclusively review the records of interest. Further collaboration is needed to upgrade the DDS to a more sophisticated analytical system and to provide a more user-friendly interface. PMID:26566352

Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

PubMed

Davis, Philip M

2013-07-01

Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

Incorporating intelligence into structured radiology reports

NASA Astrophysics Data System (ADS)

Kahn, Charles E.

2014-03-01

The new standard for radiology reporting templates being developed through the Integrating the Healthcare Enterprise (IHE) and DICOM organizations defines the storage and exchange of reporting templates as Hypertext Markup Language version 5 (HTML5) documents. The use of HTML5 enables the incorporation of "dynamic HTML," in which documents can be altered in response to their content. HTML5 documents can employ JavaScript, the HTML Document Object Model (DOM), and external web services to create intelligent reporting templates. Several reporting templates were created to demonstrate the use of scripts to perform in-template calculations and decision support. For example, a template for adrenal CT was created to compute contrast washout percentage from input values of precontrast, dynamic postcontrast, and delayed adrenal nodule attenuation values; the washout value can used to classify an adrenal nodule as a benign cortical adenoma. Dynamic templates were developed to compute volumes and apply diagnostic criteria, such as those for determination of internal carotid artery stenosis. Although reporting systems need not use a web browser to render the templates or their contents, the use of JavaScript creates innumerable opportunities to construct highly sophisticated HTML5 reporting templates. This report demonstrates the ability to incorporate dynamic content to enhance the use of radiology reporting templates.

Informatics in radiology (infoRAD): HTML and Web site design for the radiologist: a primer.

PubMed

Ryan, Anthony G; Louis, Luck J; Yee, William C

2005-01-01

A Web site has enormous potential as a medium for the radiologist to store, present, and share information in the form of text, images, and video clips. With a modest amount of tutoring and effort, designing a site can be as painless as preparing a Microsoft PowerPoint presentation. The site can then be used as a hub for the development of further offshoots (eg, Web-based tutorials, storage for a teaching library, publication of information about one's practice, and information gathering from a wide variety of sources). By learning the basics of hypertext markup language (HTML), the reader will be able to produce a simple and effective Web page that permits display of text, images, and multimedia files. The process of constructing a Web page can be divided into five steps: (a) creating a basic template with formatted text, (b) adding color, (c) importing images and multimedia files, (d) creating hyperlinks, and (e) uploading one's page to the Internet. This Web page may be used as the basis for a Web-based tutorial comprising text documents and image files already in one's possession. Finally, there are many commercially available packages for Web page design that require no knowledge of HTML.

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

Johnson, Gary E.; Sutherland, G. Bruce

The 2008 Columbia River Estuary Conference was held at the Liberty Theater in Astoria, Oregon, on April 19-20. The conference theme was ecosystem restoration. The purpose of the conference was to exchange data and information among researchers, policy-makers, and the public, i.e., interrelate science with management. Conference organizers invited presentations synthesizing material on Restoration Planning and Implementation (Session 1), Research to Reduce Restoration Uncertainties (Session 2), Wetlands and Flood Management (Session 3), Action Effectiveness Monitoring (Session 4), and Management Perspectives (Session 5). A series of three plenary talks opened the conference. Facilitated speaker and audience discussion periods were held atmore » the end of each session. Contributed posters conveyed additional data and information. These proceedings include abstracts and notes documenting questions from the audience and clarifying answers from the presenter for each talk. The proceedings also document key points from the discussion periods at the end of each session. The conference program is outlined in the agenda section. Speaker biographies are presented in Appendix A. Poster titles and authors are listed in Appendix B. A list of conference attendees is contained in Appendix C. A compact disk, attached to the back cover, contains material in hypertext-markup-language from the conference website (http://cerc.labworks.org/) and the individual presentations.« less

Automated generation of a World Wide Web-based data entry and check program for medical applications.

PubMed

Kiuchi, T; Kaihara, S

1997-02-01

The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch.

SGML by Evolution.

ERIC Educational Resources Information Center

Ensign, Chet

1993-01-01

Describes how the change to Standard Generalized Markup Language at Information Builders began with the use of SGML-like markup in text because it solved a specific problem. Notes that many additional unexpected benefits led to an investigation of converting to formal SGML-based electronic publishing. (SR)

An Overview of Genomic Sequence Variation Markup Language (GSVML)

PubMed Central

Nakaya, Jun; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Kimura, Michio

2006-01-01

Internationally accumulated genomic sequence variation data on human requires the interoperable data exchanging format. We developed the GSVML as the data exchanging format. The GSVML is human health oriented and has three categories. Analyses on the use case in human health domain and the investigation on the databases and markup languages were conducted. An interface ability to Health Level Seven Genotype Model was examined. GSVML provides a sharable platform for both clinical and research applications.

Instrument Remote Control via the Astronomical Instrument Markup Language

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528564

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Hypermedia and intelligent tutoring applications in a mission operations environment

NASA Technical Reports Server (NTRS)

Ames, Troy; Baker, Clifford

1990-01-01

Hypermedia, hypertext and Intelligent Tutoring System (ITS) applications to support all phases of mission operations are investigated. The application of hypermedia and ITS technology to improve system performance and safety in supervisory control is described - with an emphasis on modeling operator's intentions in the form of goals, plans, tasks, and actions. Review of hypermedia and ITS technology is presented as may be applied to the tutoring of command and control languages. Hypertext based ITS is developed to train flight operation teams and System Test and Operation Language (STOL). Specific hypermedia and ITS application areas are highlighted, including: computer aided instruction of flight operation teams (STOL ITS) and control center software development tools (CHIMES and STOL Certification Tool).

The "New Oxford English Dictionary" Project.

ERIC Educational Resources Information Center

Fawcett, Heather

1993-01-01

Describes the conversion of the 22,000-page Oxford English Dictionary to an electronic version incorporating a modified Standard Generalized Markup Language (SGML) syntax. Explains that the database designers chose structured markup because it supports users' data searching needs, allows textual components to be extracted or modified, and allows…

Importing MAGE-ML format microarray data into BioConductor.

PubMed

Durinck, Steffen; Allemeersch, Joke; Carey, Vincent J; Moreau, Yves; De Moor, Bart

2004-12-12

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. http://www.bioconductor.org. Open Source.

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

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

Mason, j.d.

The Department of Energy (DOE) has moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards in preference to proprietary designs promoted as "standards" by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardization (ISO)more » and the American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), which DOE has selected as the basis of its electronic management of documents. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML, and its use is likely to increase in the future. Most documents on the WWW are coded in HTML ("Hypertext Markup Language"), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Microsoft, Adobe, and Netscape, is promoting XML ("eXtensible Markup Language"), a class of SGML applications, for the future of the WWW and the basis for EC. W3C has announced its intention of discontinuing future development of HTML and replacing it with XHTML, an application of XML. In support of DOE's use of these standards, I have served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During my April 1999 trip, I convened the spring 1999 meeting of SC34 in Granada, Spain. I also attended a major conference on the use of SGML and XML. SC34 maintains and continues to enhance several standards. In addition to SGML, which is the basis of HTML and XML, SC34 also works on the Document Style Semantics and Specification Language (DSSSL), which is the basis for W3C's XSL ("eXtensible Style Language," to be used with XML) and the Hypermedia/Time-based Document Structuring Language (HyTime), which is a major influence on W3C's XLink ("XML Linking Language"). SC34 is also involved in work with ISO's TC184, Industrial Data, on the linking of STEP (the standard for the interchange of product model data) with SGML. In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Y-12 Plant. My project team in Information Technology Services developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). Supporting standards development allows DOE and the Y-12 plant both input into the process and the opportunity to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

Managing and Querying Image Annotation and Markup in XML.

PubMed

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

2010-01-01

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

Managing and Querying Image Annotation and Markup in XML

PubMed Central

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

2010-01-01

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

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

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

J. D. Mason

2001-06-18

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

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.

Analysis of the Effect of Environmental Conditions in Conducting Amphibious Assaults Using a Ship Simulator/Vessel-Response Model Proof-of-Concept Study

DTIC Science & Technology

2017-05-01

Center ESRI Environmental Systems Research Institute GIS Geographic Information System HTML Hyper -Text Markup Language LCAC Landing Craft Air... loop .” The ship simulator bridge is generic in that its layout is similar to that found in a variety of ships. As shown in Figures 17 and 18, the...information stored in the geodatabases. The Hyper -Text Markup Language (HTML) capability built into ArcMap permits a planner to click on a vessel track and

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

PubMed

Swat, M J; Moodie, S; Wimalaratne, S M; Kristensen, N R; Lavielle, M; Mari, A; Magni, P; Smith, M K; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, A C; Kaye, R; Keizer, R; Kloft, C; Kok, J N; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, H B; Parra-Guillen, Z P; Plan, E; Ribba, B; Smith, G; Trocóniz, I F; Yvon, F; Milligan, P A; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

2015-06-01

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

PubMed Central

Swat, MJ; Moodie, S; Wimalaratne, SM; Kristensen, NR; Lavielle, M; Mari, A; Magni, P; Smith, MK; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, AC; Kaye, R; Keizer, R; Kloft, C; Kok, JN; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, HB; Parra-Guillen, ZP; Plan, E; Ribba, B; Smith, G; Trocóniz, IF; Yvon, F; Milligan, PA; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

2015-01-01

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps. PMID:26225259

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2018-03-09

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML)

PubMed Central

Lechevalier, D.; Ak, R.; Ferguson, M.; Law, K. H.; Lee, Y.-T. T.; Rachuri, S.

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain. PMID:29202125

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML).

PubMed

Park, J; Lechevalier, D; Ak, R; Ferguson, M; Law, K H; Lee, Y-T T; Rachuri, S

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain.

Automated radiotherapy treatment plan integrity verification

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

Yang Deshan; Moore, Kevin L.

2012-03-15

Purpose: In our clinic, physicists spend from 15 to 60 min to verify the physical and dosimetric integrity of radiotherapy plans before presentation to radiation oncology physicians for approval. The purpose of this study was to design and implement a framework to automate as many elements of this quality control (QC) step as possible. Methods: A comprehensive computer application was developed to carry out a majority of these verification tasks in the Philips PINNACLE treatment planning system (TPS). This QC tool functions based on both PINNACLE scripting elements and PERL sub-routines. The core of this technique is the method ofmore » dynamic scripting, which involves a PERL programming module that is flexible and powerful for treatment plan data handling. Run-time plan data are collected, saved into temporary files, and analyzed against standard values and predefined logical rules. The results were summarized in a hypertext markup language (HTML) report that is displayed to the user. Results: This tool has been in clinical use for over a year. The occurrence frequency of technical problems, which would cause delays and suboptimal plans, has been reduced since clinical implementation. Conclusions: In addition to drastically reducing the set of human-driven logical comparisons, this QC tool also accomplished some tasks that are otherwise either quite laborious or impractical for humans to verify, e.g., identifying conflicts amongst IMRT optimization objectives.« less

The digital curriculum vitae.

PubMed

Galdino, Greg M; Gotway, Michael

2005-02-01

The curriculum vitae (CV) has been the traditional method for radiologists to illustrate their accomplishments in the field of medicine. Despite its presence in medicine as a standard, widely accepted means to describe one's professional career and its use for decades as an accomplice to most applications and interviews, there is relatively little written in the medical literature regarding the CV. Misrepresentation on medical students', residents', and fellows' applications has been reported. Using digital technology, CVs have the potential to be much more than printed words on paper and offers a solution to misrepresentation. Digital CVs may incorporate full-length articles, graphics, presentations, clinical images, and video. Common formats for digital CVs include CD-ROMs or DVD-ROMs containing articles (in Adobe Portable Document Format) and presentations (in Microsoft PowerPoint format) accompanying printed CVs, word processing documents with hyperlinks to articles and presentations either locally (on CD-ROMs or DVD-ROMs) or remotely (via the Internet), or hypertext markup language documents. Digital CVs afford the ability to provide more information that is readily accessible to those receiving and reviewing them. Articles, presentations, videos, images, and Internet links can be illustrated using standard file formats commonly available to all radiologists. They can be easily updated and distributed on an inexpensive media, such as a CD-ROM or DVD-ROM. With the availability of electronic articles, presentations, and information via the Internet, traditional paper CVs may soon be superseded by their electronic successors.

Dealing Your Own Hands with Hypercard.

ERIC Educational Resources Information Center

Larsen, Mark D.

1988-01-01

Extensively reviews Hypercard, a multifaceted software package for the Macintosh. HyperCard uses a language called "hypertext" which was patterned after everyday language and designed to allow flexibility in the linking and manipulation of text, graphics, and sounds. Describes one use for Hypercard in an advanced course on Latin American…

Comparing Hypertext Reading in L1 and L2: The Case of Filipino Adults

ERIC Educational Resources Information Center

Gruspe, Michael Angelo M.; Marinas, Christian Joshua L.; Villasin, Marren Nicole F.; Villanueva, Ariel Josephe Therese R.; Vizconde, Camilla J.

2015-01-01

This research probed into the reading experiences of adult readers in their first language (L1) and second language (L2). Qualitative in nature, the investigation focused on twelve (12) adult readers , six (6) males and six (6) females, whose first language is Filipino. Data were gathered through interviews and focus-group discussions. Based on…

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; Le Novére, Nicolas; Myers, Chris J.; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Waltemath, Dagmar; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528569

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

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

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.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

cluML: A markup language for clustering and cluster validity assessment of microarray data.

PubMed

Bolshakova, Nadia; Cunningham, Pádraig

2005-01-01

cluML is a new markup language for microarray data clustering and cluster validity assessment. The XML-based format has been designed to address some of the limitations observed in traditional formats, such as inability to store multiple clustering (including biclustering) and validation results within a dataset. cluML is an effective tool to support biomedical knowledge representation in gene expression data analysis. Although cluML was developed for DNA microarray analysis applications, it can be effectively used for the representation of clustering and for the validation of other biomedical and physical data that has no limitations.

Teaching physiology and the World Wide Web: electrochemistry and electrophysiology on the Internet.

PubMed

Dwyer, T M; Fleming, J; Randall, J E; Coleman, T G

1997-12-01

Students seek active learning experiences that can rapidly impart relevant information in the most convenient way possible. Computer-assisted education can now use the resources of the World Wide Web to convey the important characteristics of events as elemental as the physical properties of osmotically active particles in the cell and as complex as the nerve action potential or the integrative behavior of the intact organism. We have designed laboratory exercises that introduce first-year medical students to membrane and action potentials, as well as the more complex example of integrative physiology, using the dynamic properties of computer simulations. Two specific examples are presented. The first presents the physical laws that apply to osmotic, chemical, and electrical gradients, leading to the development of the concept of membrane potentials; this module concludes with the simulation of the ability of the sodium-potassium pump to establish chemical gradients and maintain cell volume. The second module simulates the action potential according to the Hodgkin-Huxley model, illustrating the concepts of threshold, inactivation, refractory period, and accommodation. Students can access these resources during the scheduled laboratories or on their own time via our Web site on the Internet (http./(/)phys-main.umsmed.edu) by using the World Wide Web protocol. Accurate version control is possible because one valid, but easily edited, copy of the labs exists at the Web site. A common graphical interface is possible through the use of the Hypertext mark-up language. Platform independence is possible through the logical and arithmetic calculations inherent to graphical browsers and the Javascript computer language. The initial success of this program indicates that medical education can be very effective both by the use of accurate simulations and by the existence of a universally accessible Internet resource.

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

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.

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.

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

PubMed

Kaur, Paramjit; Krishan, Kewal; Sharma, Suresh K

2018-06-01

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

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

PubMed Central

GARDNER, John; BULATOV, Vladimir; KELLY, Robert

2010-01-01

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

Field Markup Language: biological field representation in XML.

PubMed

Chang, David; Lovell, Nigel H; Dokos, Socrates

2007-01-01

With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

Standard Generalized Markup Language for self-defining structured reports.

PubMed

Kahn, C E

1999-01-01

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-09-04

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-06-01

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Enhancing L2 Vocabulary Acquisition through Implicit Reading Support Cues in E-books

ERIC Educational Resources Information Center

Liu, Yeu-Ting; Leveridge, Aubrey Neil

2017-01-01

Various explicit reading support cues, such as gloss, QR codes and hypertext annotation, have been embedded in e-books designed specifically for fostering various aspects of language development. However, explicit visual cues are not always reliably perceived as salient or effective by language learners. The current study explored the efficacy of…

The Effects of Hypertext Glosses on L2 Vocabulary Acquisition: A Meta-Analysis

ERIC Educational Resources Information Center

Yun, Jee Hwan

2010-01-01

In the field of second language acquisition (SLA), "comprehensible input" (Krashen, 1985) has been considered a critical factor to help learners acquire foreign and second languages (L2). From this perspective, the notion of extensive or free voluntary reading (Day & Bamford, 1998; Krashen, 1993) has emerged that L2 learners should be given more…

Teaching XBRL to Graduate Business Students: A Hands-On Approach

ERIC Educational Resources Information Center

Pinsker, Robert

2004-01-01

EXtensible Business Reporting Language (XBRL) is a non-proprietary, computer language that has many uses. Known primarily as the Extensible Markup Language (XML) for business reporting, XBRL allows entities to report their business information (i.e., financial statements, announcements, etc.) on the Internet and communicate with other entities'…

XML Schema Languages: Beyond DTD.

ERIC Educational Resources Information Center

Ioannides, Demetrios

2000-01-01

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

World Wide Web and Internet: applications for radiologists.

PubMed

Wunderbaldinger, P; Schima, W; Turetschek, K; Helbich, T H; Bankier, A A; Herold, C J

1999-01-01

Global exchange of information is one of the major sources of scientific progress in medicine. For management of the rapidly growing body of medical information, computers and their applications have become an indispensable scientific tool. Approximately 36 million computer users are part of a worldwide network called the Internet or "information highway" and have created a new infrastructure to promote rapid and efficient access to medical, and thus also to radiological, information. With the establishment of the World Wide Web (WWW) by a consortium of computer users who used a standardized, nonproprietary syntax termed HyperText Markup Language (HTML) for composing documents, it has become possible to provide interactive multimedia presentations to a wide audience. The extensive use of images in radiology makes education, worldwide consultation (review) and scientific presentation via the Internet a major beneficiary of this technical development. This is possible, since both information (text) as well as medical images can be transported via the Internet. Presently, the Internet offers an extensive database for radiologists. Since many radiologists and physicians have to be considered "Internet novices" and, hence, cannot yet avail themselves of the broad spectrum of the Internet, the aim of this article is to present a general introduction to the WWW/Internet and its applications for radiologists. All Internet sites mentioned in this article can be found at the following Internet address: http://www.univie.ac. at/radio/radio.html (Department of Radiology, University of Vienna)

Computer-Based and Paper-Based Reading Comprehension in Adolescents with Typical Language Development and Language-Learning Disabilities

ERIC Educational Resources Information Center

Srivastava, Pradyumn; Gray, Shelley

2012-01-01

Purpose: With the global expansion of technology, our reading platform has shifted from traditional text to hypertext, yet little consideration has been given to how this shift might help or hinder students' reading comprehension. The purpose of this study was to compare reading comprehension of computer-based and paper-based texts in adolescents…

Hypertext-based computer vision teaching packages

NASA Astrophysics Data System (ADS)

Marshall, A. David

1994-10-01

The World Wide Web Initiative has provided a means for providing hypertext and multimedia based information across the whole INTERNET. Many applications have been developed on such http servers. At Cardiff we have developed a http hypertext based multimedia server, the Cardiff Information Server, using the widely available Mosaic system. The server provides a variety of information ranging from the provision of teaching modules, on- line documentation, timetables for departmental activities to more light hearted hobby interests. One important and novel development to the server has been the development of courseware facilities. This ranges from the provision of on-line lecture notes, exercises and their solutions to more interactive teaching packages. A variety of disciplines have benefitted notably Computer Vision, and Image Processing but also C programming, X Windows, Computer Graphics and Parallel Computing. This paper will address the issues of the implementation of the Computer Vision and Image Processing packages, the advantages gained from using a hypertext based system and also will relate practical experiences of using the packages in a class environment. The paper addresses issues of how best to provide information in such a hypertext based system and how interactive image processing packages can be developed and integrated into courseware. The suite of tools developed facilitates a flexible and powerful courseware package that has proved popular in the classroom and over the Internet. The paper will also detail many future developments we see possible. One of the key points raised in the paper is that Mosaic's hypertext language (html) is extremely powerful and yet relatively straightforward to use. It is also possible to link in Unix calls so that programs and shells can be executed. This provides a powerful suite of utilities that can be exploited to develop many packages.

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

The primary objective of the proposed Earth Science Markup Language (ESML) research is to transition from design to application. The resulting schema and prototype software will foster community acceptance for the "define once, use anywhere" concept central to ESML. Supporting goals include: 1. Refinement of the ESML schema and software libraries in cooperation with the user community. 2. Application of the ESML schema and software libraries to a variety of Earth science data sets and analysis tools. 3. Development of supporting prototype software for enhanced ease of use. 4. Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate. 5. Widespread publication of the ESML approach, schema, and software.

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

PubMed

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

2005-01-01

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

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

PubMed

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

2007-01-01

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

"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…

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

PubMed

Bergmann, Frank T; Cooper, Jonathan; König, Matthias; Moraru, Ion; Nickerson, David; Le Novère, Nicolas; Olivier, Brett G; Sahle, Sven; Smith, Lucian; Waltemath, Dagmar

2018-03-19

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

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)

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

PubMed

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

2005-08-01

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

XBRL: Beyond Basic XML

ERIC Educational Resources Information Center

VanLengen, Craig Alan

2010-01-01

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

Networking observers and observatories with remote telescope markup language

NASA Astrophysics Data System (ADS)

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

2006-06-01

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

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

PubMed

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

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.

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

PubMed

Zi, Zhike

2011-04-01

Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

PubMed Central

2012-01-01

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

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

DTIC Science & Technology

2006-06-01

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

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

PubMed

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

2004-01-01

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

A Google Earth Grand Tour of the Terrestrial Planets

ERIC Educational Resources Information Center

De Paor, Declan; Coba, Filis; Burgin, Stephen

2016-01-01

Google Earth is a powerful instructional resource for geoscience education. We have extended the virtual globe to include all terrestrial planets. Downloadable Keyhole Markup Language (KML) files (Google Earth's scripting language) associated with this paper include lessons about Mercury, Venus, the Moon, and Mars. We created "grand…

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

ERIC Educational Resources Information Center

Mohler, James L.

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

Hypermedia 1990 structured Hypertext tutorial

NASA Technical Reports Server (NTRS)

Johnson, J. Scott

1990-01-01

Hypermedia 1990 structured Hypertext tutorial is presented in the form of view-graphs. The following subject areas are covered: structured hypertext; analyzing hypertext documents for structure; designing structured hypertext documents; creating structured hypertext applications; structuring service and repair documents; maintaining structured hypertext documents; and structured hypertext conclusion.

Defining Linkages between the GSC and NSF's LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes

Treesearch

Inigo San Gil; Wade Sheldon; Tom Schmidt; Mark Servilla; Raul Aguilar; Corinna Gries; Tanya Gray; Dawn Field; James Cole; Jerry Yun Pan; Giri Palanisamy; Donald Henshaw; Margaret O' Brien; Linda Kinkel; Kathrine McMahon; Renzo Kottmann; Linda Amaral-Zettler; John Hobbie; Philip Goldstein; Robert P. Guralnick; James Brunt; William K. Michener

2008-01-01

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML)....

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Improving the Interoperability of Disaster Models: a Case Study of Proposing Fireml for Forest Fire Model

NASA Astrophysics Data System (ADS)

Jiang, W.; Wang, F.; Meng, Q.; Li, Z.; Liu, B.; Zheng, X.

2018-04-01

This paper presents a new standardized data format named Fire Markup Language (FireML), extended by the Geography Markup Language (GML) of OGC, to elaborate upon the fire hazard model. The proposed FireML is able to standardize the input and output documents of a fire model for effectively communicating with different disaster management systems to ensure a good interoperability. To demonstrate the usage of FireML and testify its feasibility, an adopted forest fire spread model being compatible with FireML is described. And a 3DGIS disaster management system is developed to simulate the dynamic procedure of forest fire spread with the defined FireML documents. The proposed approach will enlighten ones who work on other disaster models' standardization work.

Consistent data recording across a health system and web-enablement allow service quality comparisons: online data for commissioning dermatology services.

PubMed

Dmitrieva, Olga; Michalakidis, Georgios; Mason, Aaron; Jones, Simon; Chan, Tom; de Lusignan, Simon

2012-01-01

A new distributed model of health care management is being introduced in England. Family practitioners have new responsibilities for the management of health care budgets and commissioning of services. There are national datasets available about health care providers and the geographical areas they serve. These data could be better used to assist the family practitioner turned health service commissioners. Unfortunately these data are not in a form that is readily usable by these fledgling family commissioning groups. We therefore Web enabled all the national hospital dermatology treatment data in England combining it with locality data to provide a smart commissioning tool for local communities. We used open-source software including the Ruby on Rails Web framework and MySQL. The system has a Web front-end, which uses hypertext markup language cascading style sheets (HTML/CSS) and JavaScript to deliver and present data provided by the database. A combination of advanced caching and schema structures allows for faster data retrieval on every execution. The system provides an intuitive environment for data analysis and processing across a large health system dataset. Web-enablement has enabled data about in patients, day cases and outpatients to be readily grouped, viewed, and linked to other data. The combination of web-enablement, consistent data collection from all providers; readily available locality data; and a registration based primary system enables the creation of data, which can be used to commission dermatology services in small areas. Standardized datasets collected across large health enterprises when web enabled can readily benchmark local services and inform commissioning decisions.

GIS based application tool -- history of East India Company

NASA Astrophysics Data System (ADS)

Phophaliya, Sudhir

The emphasis of the thesis is to build an intuitive and robust GIS (Geographic Information systems) Tool which gives an in depth information on history of East India Company. The GIS tool also incorporates various achievements of East India Company which helped to establish their business all over world especially India. The user has the option to select these movements and acts by clicking on any of the marked states on the World map. The World Map also incorporates key features for East India Company like landing of East India Company in India, Darjeeling Tea Establishment, East India Company Stock Redemption Act etc. The user can know more about these features simply by clicking on each of them. The primary focus of the tool is to give the user a unique insight about East India Company; for this the tool has several HTML (Hypertext markup language) pages which the user can select. These HTML pages give information on various topics like the first Voyage, Trade with China, 1857 Revolt etc. The tool has been developed in JAVA. For the Indian map MOJO (Map Objects Java Objects) is used. MOJO is developed by ESRI. The major features shown on the World map was designed using MOJO. MOJO made it easy to incorporate the statistical data with these features. The user interface was intentionally kept simple and easy to use. To keep the user engaged, key aspects are explained using HTML pages. The idea is that pictures will help the user garner interest in the history of East India Company.

Automatic Text Decomposition and Structuring.

ERIC Educational Resources Information Center

Salton, Gerard; And Others

1996-01-01

Text similarity measurements are used to determine relationships between natural-language texts and text excerpts. The resulting linked hypertext maps can be broken down into text segments and themes used to identify different text types and structures, leading to improved information access and utilization. Examples are provided for text…

Feral Hypertext: When Hypertext Literature Escapes Control

NASA Astrophysics Data System (ADS)

Rettberg, Jill Walker

This article explores the historical development of hypertext, arguing that we have seen a transition from early visions and implementations of hypertext that primarily dealt with using hypertext to gain greater control over knowledge and ideas, to today's messy web. Pre-web hypertext can be seen as a domesticated species bred in captivity. On the web, however, some breeds of hypertext have gone feral. Feral hypertext is no longer tame and domesticated, but is fundamentally out of our control. In order to understand and work with feral hypertext, we need to accept this and think more as hunter-gatherers than as the farmers we were for domesticated hypertext. The article discusses hypertext in general with an emphasis on literary and creative hypertext practice.

Genomic Sequence Variation Markup Language (GSVML).

PubMed

Nakaya, Jun; Kimura, Michio; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Tanaka, Hiroshi

2010-02-01

With the aim of making good use of internationally accumulated genomic sequence variation data, which is increasing rapidly due to the explosive amount of genomic research at present, the development of an interoperable data exchange format and its international standardization are necessary. Genomic Sequence Variation Markup Language (GSVML) will focus on genomic sequence variation data and human health applications, such as gene based medicine or pharmacogenomics. We developed GSVML through eight steps, based on case analysis and domain investigations. By focusing on the design scope to human health applications and genomic sequence variation, we attempted to eliminate ambiguity and to ensure practicability. We intended to satisfy the requirements derived from the use case analysis of human-based clinical genomic applications. Based on database investigations, we attempted to minimize the redundancy of the data format, while maximizing the data covering range. We also attempted to ensure communication and interface ability with other Markup Languages, for exchange of omics data among various omics researchers or facilities. The interface ability with developing clinical standards, such as the Health Level Seven Genotype Information model, was analyzed. We developed the human health-oriented GSVML comprising variation data, direct annotation, and indirect annotation categories; the variation data category is required, while the direct and indirect annotation categories are optional. The annotation categories contain omics and clinical information, and have internal relationships. For designing, we examined 6 cases for three criteria as human health application and 15 data elements for three criteria as data formats for genomic sequence variation data exchange. The data format of five international SNP databases and six Markup Languages and the interface ability to the Health Level Seven Genotype Model in terms of 317 items were investigated. GSVML was developed as a potential data exchanging format for genomic sequence variation data exchange focusing on human health applications. The international standardization of GSVML is necessary, and is currently underway. GSVML can be applied to enhance the utilization of genomic sequence variation data worldwide by providing a communicable platform between clinical and research applications. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

A general UNIX interface for biocomputing and network information retrieval software.

PubMed

Kiong, B K; Tan, T W

1993-10-01

We describe a UNIX program, HYBROW, which can integrate without modification a wide range of UNIX biocomputing and network information retrieval software. HYBROW works in conjunction with a separate set of ASCII files containing embedded hypertext-like links. The program operates like a hypertext browser featuring five basic links: file link, execute-only link, execute-display link, directory-browse link and field-filling link. Useful features of the interface may be developed using combinations of these links with simple shell scripts and examples of these are briefly described. The system manager who supports biocomputing users should find the program easy to maintain, and useful in assisting new and infrequent users; it is also simple to incorporate new programs. Moreover, the individual user can customize the interface, create dynamic menus, hypertext a document, invoke shell scripts and new programs simply with a basic understanding of the UNIX operating system and any text editor. This program was written in C language and uses the UNIX curses and termcap libraries. It is freely available as a tar compressed file (by anonymous FTP from nuscc.nus.sg).

Effect of Hypertextual Reading on Academic Success and Comprehension Skills

ERIC Educational Resources Information Center

Durukan, Erhan

2014-01-01

As computer technology developed, hypertexts emerged as an influential environment for developing language skills. This study aims to evaluate a text prepared in a hypertextual environment and its effects on academic success and comprehension skills. In this study, "preliminary test final test control group experimental pattern" was used…

Introducing Today's SGML.

ERIC Educational Resources Information Center

Gilmore, Elizabeth

1993-01-01

Describes the fundamental concepts and potential of Standard General Markup Language (SGML), a system that allows computer users to exchange, reuse, and reformat information without constraint. Illustrates the concepts of SGML through a simple example. (SR)

A New Method of Viewing Attachment Document of eMail on Various Mobile Devices

NASA Astrophysics Data System (ADS)

Ko, Heeae; Seo, Changwoo; Lim, Yonghwan

As the computing power of the mobile devices is improving rapidly, many kinds of web services are also available in mobile devices just as Email service. Mobile Mail Service began early, but this service is mostly limited in some specified mobile devices such as Smart Phone. That is a limitation that users have to purchase specified phone to be benefited from Mobile Mail Service. In this paper, it uses DIDL (digital item declaration language) markup type defined in MPEG-21 and MobileGate Server, and solved this problem. DIDL could be converted to other markup types which are displayed by mobile devices. By transforming PC Web Mail contents including attachment document to DIDL markup through MobileGate Server, the Mobile Mail Service could be available for all kinds of mobile devices.

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"…

Nassi-Schneiderman Diagram in HTML Based on AML

ERIC Educational Resources Information Center

Menyhárt, László

2013-01-01

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

XML DTD and Schemas for HDF-EOS

NASA Technical Reports Server (NTRS)

Ullman, Richard; Yang, Jingli

2008-01-01

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

Running MONET and SALT with Remote Telescope Markup Language 3.0

NASA Astrophysics Data System (ADS)

Hessman, F. V.; Romero, E.

2003-05-01

Complex robotic and service observations in heterogenous networks of telescopes require a common telescopic lingua franca for the description and transport of observing requests and results. Building upon the experience gained within the Hands-On Universe (HOU) and advanced amateur communities with Remote Telescope Markup Language (RTML) Version 2.1 (http://sunra.lbl.gov/rtml), we have implemented a revised RTML syntax (Version 3.0) which is fully capable of - running the two 1.2m MONET robotic telescopes for a very inhomogeneous clientel from 3 research institutions and high school classes all over the world; - connecting MONET to the HOU telescope network; - connecting MONET as a trigger to the 11m SALT telescope; - providing all the objects needed to perform and document internet-based user support, ranging all the way from proposal submission and time-allocation to observation reports.

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

PubMed

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

2004-12-01

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

Instrument Remote Control Application Framework

NASA Technical Reports Server (NTRS)

Ames, Troy; Hostetter, Carl F.

2006-01-01

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

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

PubMed

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

2003-01-01

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

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

PubMed Central

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

2003-01-01

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

Gene Fusion Markup Language: a prototype for exchanging gene fusion data.

PubMed

Kalyana-Sundaram, Shanker; Shanmugam, Achiraman; Chinnaiyan, Arul M

2012-10-16

An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses.

C3I and Modelling and Simulation (M&S) Interoperability

DTIC Science & Technology

2004-03-01

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

The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation model.

PubMed

Mongkolwat, Pattanasak; Kleper, Vladimir; Talbot, Skip; Rubin, Daniel

2014-12-01

Knowledge contained within in vivo imaging annotated by human experts or computer programs is typically stored as unstructured text and separated from other associated information. The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation information model is an evolution of the National Institute of Health's (NIH) National Cancer Institute's (NCI) Cancer Bioinformatics Grid (caBIG®) AIM model. The model applies to various image types created by various techniques and disciplines. It has evolved in response to the feedback and changing demands from the imaging community at NCI. The foundation model serves as a base for other imaging disciplines that want to extend the type of information the model collects. The model captures physical entities and their characteristics, imaging observation entities and their characteristics, markups (two- and three-dimensional), AIM statements, calculations, image source, inferences, annotation role, task context or workflow, audit trail, AIM creator details, equipment used to create AIM instances, subject demographics, and adjudication observations. An AIM instance can be stored as a Digital Imaging and Communications in Medicine (DICOM) structured reporting (SR) object or Extensible Markup Language (XML) document for further processing and analysis. An AIM instance consists of one or more annotations and associated markups of a single finding along with other ancillary information in the AIM model. An annotation describes information about the meaning of pixel data in an image. A markup is a graphical drawing placed on the image that depicts a region of interest. This paper describes fundamental AIM concepts and how to use and extend AIM for various imaging disciplines.

Restructuring an EHR system and the Medical Markup Language (MML) standard to improve interoperability by archetype technology.

PubMed

Kobayashi, Shinji; Kume, Naoto; Yoshihara, Hiroyuki

2015-01-01

In 2001, we developed an EHR system for regional healthcare information inter-exchange and to provide individual patient data to patients. This system was adopted in three regions in Japan. We also developed a Medical Markup Language (MML) standard for inter- and intra-hospital communications. The system was built on a legacy platform, however, and had not been appropriately maintained or updated to meet clinical requirements. To improve future maintenance costs, we reconstructed the EHR system using archetype technology on the Ruby on Rails platform, and generated MML equivalent forms from archetypes. The system was deployed as a cloud-based system for preliminary use as a regional EHR. The system now has the capability to catch up with new requirements, maintaining semantic interoperability with archetype technology. It is also more flexible than the legacy EHR system.

XML Based Scientific Data Management Facility

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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.

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

PubMed

Zi, Zhike; Klipp, Edda

2006-11-01

The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system. http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

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).

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

PubMed

Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

2004-06-01

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Computerization of guidelines: towards a "guideline markup language".

PubMed

Dart, T; Xu, Y; Chatellier, G; Degoulet, P

2001-01-01

Medical decision making is one of the most difficult daily tasks for physicians. Guidelines have been designed to reduce variance between physicians in daily practice, to improve patient outcomes and to control costs. In fact, few physicians use guidelines in daily practice. A way to ease the use of guidelines is to implement computerised guidelines (computer reminders). We present in this paper a method of computerising guidelines. Our objectives were: 1) to propose a generic model that can be instantiated for any specific guidelines; 2) to use eXtensible Markup Language (XML) as a guideline representation language to instantiate the generic model for a specific guideline. Our model is an object representation of a clinical algorithm, it has been validated by running two different guidelines issued by a French official Agency. In spite of some limitations, we found that this model is expressive enough to represent complex guidelines devoted to diabetes and hypertension management. We conclude that XML can be used as a description format to structure guidelines and as an interface between paper-based guidelines and computer applications.

Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

NASA Technical Reports Server (NTRS)

Brian, Geoffrey J.; Jackson, E. Bruce

2011-01-01

The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) is a syntactical language for exchanging flight vehicle dynamic model data. It provides a framework for encoding entire flight vehicle dynamic model data packages for exchange and/or long-term archiving. Version 2.0.1 of DAVE-ML provides much of the functionality envisioned for exchanging aerospace vehicle data; however, it is limited in only supporting scalar time-independent data. Additional functionality is required to support vector and matrix data, abstracting sub-system models, detailing dynamics system models (both discrete and continuous), and defining a dynamic data format (such as time sequenced data) for validation of dynamics system models and vehicle simulation packages. Extensions to DAVE-ML have been proposed to manage data as vectors and n-dimensional matrices, and record dynamic data in a compatible form. These capabilities will improve the clarity of data being exchanged, simplify the naming of parameters, and permit static and dynamic data to be stored using a common syntax within a single file; thereby enhancing the framework provided by DAVE-ML for exchanging entire flight vehicle dynamic simulation models.

Enhancement of CLAIM (clinical accounting information) for a localized Chinese version.

PubMed

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

2005-10-01

CLinical Accounting InforMation (CLAIM) is a standard for the exchange of data between patient accounting systems and electronic medical record (EMR) systems. It uses eXtensible Markup Language (XML) as a meta-language and was developed in Japan. CLAIM is subordinate to the Medical Markup Language (MML) standard, which allows the exchange of medical data between different medical institutions. It has inherited the basic structure of MML 2.x and the current version, version 2.1, contains two modules and nine data definition tables. In China, no data exchange standard yet exists that links EMR systems to accounting systems. Taking advantage of CLAIM's flexibility, we created a localized Chinese version based on CLAIM 2.1. Since Chinese receipt systems differ from those of Japan, some information such as prescription formats, etc. are also different from those in Japan. Two CLAIM modules were re-engineered and six data definition tables were either added or redefined. The Chinese version of CLAIM takes local needs into account, and consequently it is now possible to transfer data between the patient accounting systems and EMR systems of Chinese medical institutions effectively.

Gene Fusion Markup Language: a prototype for exchanging gene fusion data

PubMed Central

2012-01-01

Background An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Results Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. Conclusion The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses. PMID:23072312

Looking Tasks Online: Utilizing Webcams to Collect Video Data from Home

PubMed Central

Semmelmann, Kilian; Hönekopp, Astrid; Weigelt, Sarah

2017-01-01

Online experimentation is emerging as a new methodology within classical data acquisition in psychology. It allows for easy, fast, broad, and cheap data conduction from the comfort of people’s homes. To add another method to the array of available tools, here we used recent developments in web technology to investigate the technical feasibility of online HyperText Markup Language-5/JavaScript-based video data recording. We employed a preferential looking task with children between 4 and 24 months. Parents and their children participated from home through a three-stage process: First, interested adults registered and took pictures through a webcam-based photo application. In the second step, we edited the pictures and integrated them into the design. Lastly, participants returned to the website and the video data acquisition took place through their webcam. In sum, we were able to create and employ the video recording application with participants as young as 4 months old. Quality-wise, no participant had to be removed due to the framerate or quality of videos and only 7% of data was excluded due to behavioral factors (lack of concentration). Results-wise, interrater reliability of rated looking side (left/right) showed a high agreement between raters, Fleiss’ Kappa, κ = 0.97, which can be translated to sufficient data quality for further analyses. With regard to on-/off-screen attention attribution, we found that children lost interest after about 10 s after trial onset using a static image presentation or 60 s total experimental time. Taken together, we were able to show that online video data recording is possible and viable for developmental psychology and beyond. PMID:28955284

Looking Tasks Online: Utilizing Webcams to Collect Video Data from Home.

PubMed

Semmelmann, Kilian; Hönekopp, Astrid; Weigelt, Sarah

2017-01-01

Online experimentation is emerging as a new methodology within classical data acquisition in psychology. It allows for easy, fast, broad, and cheap data conduction from the comfort of people's homes. To add another method to the array of available tools, here we used recent developments in web technology to investigate the technical feasibility of online HyperText Markup Language-5/JavaScript-based video data recording. We employed a preferential looking task with children between 4 and 24 months. Parents and their children participated from home through a three-stage process: First, interested adults registered and took pictures through a webcam-based photo application. In the second step, we edited the pictures and integrated them into the design. Lastly, participants returned to the website and the video data acquisition took place through their webcam. In sum, we were able to create and employ the video recording application with participants as young as 4 months old. Quality-wise, no participant had to be removed due to the framerate or quality of videos and only 7% of data was excluded due to behavioral factors (lack of concentration). Results-wise, interrater reliability of rated looking side (left/right) showed a high agreement between raters, Fleiss' Kappa, κ = 0.97, which can be translated to sufficient data quality for further analyses. With regard to on-/off-screen attention attribution, we found that children lost interest after about 10 s after trial onset using a static image presentation or 60 s total experimental time. Taken together, we were able to show that online video data recording is possible and viable for developmental psychology and beyond.

WebGIS Platform Adressed to Forest Fire Management Methodologies

NASA Astrophysics Data System (ADS)

André Ramos-Simões, Nuno; Neto Paixão, Helena Maria; Granja Martins, Fernando Miguel; Pedras, Celestina; Lança, Rui; Silva, Elisa; Jordán, António; Zavala, Lorena; Soares, Cristina

2015-04-01

Forest fires are one of the natural disasters that causes more damages in nature, as well as high material costs, and sometimes, a significant losses in human lives. In summer season, when high temperatures are attained, fire may rapidly progress and destroy vast areas of forest and also rural and urban areas. The forest fires have effect on forest species, forest composition and structure, soil properties and soil capacity for nutrient retention. In order to minimize the negative impact of the forest fires in the environment, many studies have been developed, e.g. Jordán et al (2009), Cerdà & Jordán (2010), and Gonçalves & Vieira (2013). Nowadays, Remote Sensing (RS) and Geographic Information System (GIS) technologies are used as support tools in fire management decisions, namely during the fire, but also before and after. This study presents the development of a user-friendly WebGIS dedicated to share data, maps and provide updated information on forest fire management for stakeholders in Iberia Peninsula. The WebGIS platform was developed with ArcGIS Online, ArcGIS for Desktop; HyperText Markup Language (HTML) and Javascript. This platform has a database that includes spatial and alphanumeric information, such as: origin, burned areas, vegetation change over time, terrain natural slope, land use, soil erosion and fire related hazards. The same database contains also the following relevant information: water sources, forest tracks and traffic ways, lookout posts and urban areas. The aim of this study is to provide the authorities with a tool to assess risk areas and manage more efficiently forest fire hazards, giving more support to their decisions and helping the populations when facing this kind of phenomena.

The tissue micro-array data exchange specification: a web based experience browsing imported data

PubMed Central

Nohle, David G; Hackman, Barbara A; Ayers, Leona W

2005-01-01

Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. Conclusion Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA. PMID:16086837

Hypertext Glosses for Foreign Language Reading Comprehension and Vocabulary Acquisition: Effects of Assessment Methods

ERIC Educational Resources Information Center

Chen, I-Jung

2016-01-01

This study compared how three different gloss modes affected college students' L2 reading comprehension and vocabulary acquisition. The study also compared how results on comprehension and vocabulary acquisition may differ depending on the four assessment methods used. A between-subjects design was employed with three groups of Mandarin-speaking…

Addressing hypertext design and conversion issues

NASA Technical Reports Server (NTRS)

Glusko, Robert J.

1990-01-01

Hypertext is a network of information units connected by relational links. A hypertext system is a configuration of hardware and software that presents a hypertext to users and allows them to manage and access the information that it contains. Hypertext is also a user interface concept that closely supports the ways that people use printed information. Hypertext concepts encourage modularity and the elimination of redundancy in data bases because information can be stored only once but viewed in any appropriate context. Hypertext is such a hot idea because it is an enabling technology in that workstations and personal computers finally provide enough local processing power for hypertext user interfaces.

Why SGML? Why Now?

ERIC Educational Resources Information Center

Marcoux, Yves; Sevigny, Martin

1997-01-01

Defines Standard Generalized Markup Language (SGML), a format for electronic documents that provides documentary information for efficient accessibility, dissemination, and preservation. Compares SGML to Open Document Architecture (ODA) based on standards by the International Organization for Standardization (ISO), and describes the principles and…

Knowledge Provenance in Semantic Wikis

NASA Astrophysics Data System (ADS)

Ding, L.; Bao, J.; McGuinness, D. L.

2008-12-01

Collaborative online environments with a technical Wiki infrastructure are becoming more widespread. One of the strengths of a Wiki environment is that it is relatively easy for numerous users to contribute original content and modify existing content (potentially originally generated by others). As more users begin to depend on informational content that is evolving by Wiki communities, it becomes more important to track the provenance of the information. Semantic Wikis expand upon traditional Wiki environments by adding some computationally understandable encodings of some of the terms and relationships in Wikis. We have developed a semantic Wiki environment that expands a semantic Wiki with provenance markup. Provenance of original contributions as well as modifications is encoded using the provenance markup component of the Proof Markup Language. The Wiki environment provides the provenance markup automatically, thus users are not required to make specific encodings of author, contribution date, and modification trail. Further, our Wiki environment includes a search component that understands the provenance primitives and thus can be used to provide a provenance-aware search facility. We will describe the knowledge provenance infrastructure of our Semantic Wiki and show how it is being used as the foundation of our group web site as well as a number of project web sites.

Hypertext: Link to the Future.

ERIC Educational Resources Information Center

Marmion, Dan

1990-01-01

Describes the origins of hypertext and reviews the history of the concept of nonsequential access to information that led to hypertext. Technological developments that have been combined with hypertext are discussed, including workstations, video and laser disk technology, and microcomputers; and library applications of hypertext and hypermedia…

Hypertext and Information Retrieval.

ERIC Educational Resources Information Center

Smith, Karen E.; And Others

1988-01-01

An overview of hypertext and hypermedia is followed by a description of the Intermedia system, and possibilities for using hypertext in the information industry are explored. A sidebar discusses information retrieval in the humanities using hypertext, and a 58-item annotated bibliography on hypertext is presented. (7 references) (MES)

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.

Dictionary as Database.

ERIC Educational Resources Information Center

Painter, Derrick

1996-01-01

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Automating hypertext for decision support

NASA Technical Reports Server (NTRS)

Bieber, Michael

1990-01-01

A decision support system (DSS) shell is being constructed that can support applications in a variety of fields, e.g., engineering, manufacturing, finance. The shell provides a hypertext-style interface for 'navigating' among DSS application models, data, and reports. The traditional notion of hypertext had to be enhanced. Hypertext normally requires manually, pre-defined links. A DSS shell, however, requires that hypertext connections to be built 'on the fly'. The role of hypertext is discussed in augmenting DSS applications and the decision making process. Also discussed is how hypertext nodes, links, and link markers tailored to an arbitrary DSS application were automatically generated.

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

Using XML and Java for Astronomical Instrument Control

NASA Astrophysics Data System (ADS)

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

1999-12-01

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

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.

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

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

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

The E-Book: Pipe Dream or Potential Disaster?

ERIC Educational Resources Information Center

Dorman, David

1999-01-01

Discusses the development of electronic books and considers marketing and distribution, rights management, and technical standards. Economic and institutional relationships, copyrights, Extensible Markup Language (XML), access to content, free access versus fees, preservation versus loss of control over long-term storage and access, and trusted…

Designing and Managing Your Digital Library.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

Discusses digital libraries and Web site design issues. Highlights include accessibility issues, including standards, markup languages like HTML and XML, and metadata; building virtual communities; the use of Web portals for customized delivery of information; quality assurance tools, including data mining; and determining user needs, including…

SCOPIC Design and Overview

ERIC Educational Resources Information Center

Barth, Danielle; Evans, Nicholas

2017-01-01

This paper provides an overview of the design and motivation for creating the Social Cognition Parallax Interview Corpus (SCOPIC), an open-ended, accessible corpus that balances the need for language-specific annotation with typologically-calibrated markup. SCOPIC provides richly annotated data, focusing on functional categories relevant to social…

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…

Accessing Electronic Theses: Progress?

ERIC Educational Resources Information Center

Tennant, Roy

2000-01-01

Describes various ways by which universities provide access to their electronic theses and dissertations (ETDs), discussing UMI (University Microfilms International), XML (eXtensible Markup Language), and other formats. Discusses key leaders--national and international--in the ETD effort. Outlines the two main methods for locating ETDs. Presents a…

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

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.

Converting CSV Files to RKSML Files

NASA Technical Reports Server (NTRS)

Trebi-Ollennu, Ashitey; Liebersbach, Robert

2009-01-01

A computer program converts, into a format suitable for processing on Earth, files of downlinked telemetric data pertaining to the operation of the Instrument Deployment Device (IDD), which is a robot arm on either of the Mars Explorer Rovers (MERs). The raw downlinked data files are in comma-separated- value (CSV) format. The present program converts the files into Rover Kinematics State Markup Language (RKSML), which is an Extensible Markup Language (XML) format that facilitates representation of operations of the IDD and enables analysis of the operations by means of the Rover Sequencing Validation Program (RSVP), which is used to build sequences of commanded operations for the MERs. After conversion by means of the present program, the downlinked data can be processed by RSVP, enabling the MER downlink operations team to play back the actual IDD activity represented by the telemetric data against the planned IDD activity. Thus, the present program enhances the diagnosis of anomalies that manifest themselves as differences between actual and planned IDD activities.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

PubMed Central

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-01-01

Background It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. Results This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. Conclusion SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes. PMID:18706080

AllerML: markup language for allergens.

PubMed

Ivanciuc, Ovidiu; Gendel, Steven M; Power, Trevor D; Schein, Catherine H; Braun, Werner

2011-06-01

Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. Copyright © 2011 Elsevier Inc. All rights reserved.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

PubMed

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-08-15

It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

PubMed

Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

2010-09-01

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

AllerML: Markup Language for Allergens

PubMed Central

Ivanciuc, Ovidiu; Gendel, Steven M.; Power, Trevor D.; Schein, Catherine H.; Braun, Werner

2011-01-01

Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. PMID:21420460

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

PubMed Central

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

2007-01-01

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

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

PubMed

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

2007-03-06

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

Global Situational Awareness with Free Tools

DTIC Science & Technology

2015-01-15

Client Technical Solutions • Software Engineering Measurement and Analysis • Architecture Practices • Product Line Practice • Team Software Process...multiple data sources • Snort (Snorby on Security Onion ) • Nagios • SharePoint RSS • Flow • Others • Leverage standard data formats • Keyhole Markup Language

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…

Applying Data Mining Principles to Library Data Collection.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

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

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.…

Cornerstone: Foundational Models and Services for Integrated Battle Planning

DTIC Science & Technology

2012-06-01

We close with a summary of future planned research. 3 Cross-Domain Knowledge Representation One of the primary reasons behind the...mission data using Google Earth to display the results of a Keyhole Markup Language (KML) mission data translator. Finally, we successfully ran Thread 1

BioC: a minimalist approach to interoperability for biomedical text processing

PubMed Central

Comeau, Donald C.; Islamaj Doğan, Rezarta; Ciccarese, Paolo; Cohen, Kevin Bretonnel; Krallinger, Martin; Leitner, Florian; Lu, Zhiyong; Peng, Yifan; Rinaldi, Fabio; Torii, Manabu; Valencia, Alfonso; Verspoor, Karin; Wiegers, Thomas C.; Wu, Cathy H.; Wilbur, W. John

2013-01-01

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net/ PMID:24048470

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

PubMed

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

2013-01-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2000-10-01

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

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.

Ontario Hydro and SGML.

ERIC Educational Resources Information Center

Rockley, Ann

1993-01-01

Describes how an analysis of Ontario Hydro's conversion of 20,000 pages of paper manuals to online documentation established the scope of the project, provided a set of design criteria, and recommended the use of Standard Generalized Markup Language to create the new documentation and the purchase of the "Dinatext" program to produce it.…

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…

Assessing Place Location Knowledge Using a Virtual Globe

ERIC Educational Resources Information Center

Zhu, Liangfeng; Pan, Xin; Gao, Gongcheng

2016-01-01

Advances in the Google Earth virtual globe and the concomitant Keyhole Markup Language (KML) are providing educators with a convenient platform to cultivate and assess one's place location knowledge (PLK). This article presents a general framework and associated implementation methods for the online testing of PLK using Google Earth. The proposed…

Searchers Net Treasure in Monterey.

ERIC Educational Resources Information Center

McDermott, Irene E.

1999-01-01

Reports on Web keyword searching, metadata, Dublin Core, Extensible Markup Language (XML), metasearch engines (metasearch engines search several Web indexes and/or directories and/or Usenet and/or specific Web sites), and the Year 2000 (Y2K) dilemma, all topics discussed at the second annual Internet Librarian Conference sponsored by Information…

Making Technology Work for Scholarship: Investing in the Data.

ERIC Educational Resources Information Center

Hockey, Susan

This paper examines issues related to how providers and consumers can make the best use of electronic information, focusing on the humanities. Topics include: new technology or old; electronic text and data formats; Standard Generalized Markup Language (SGML); text encoding initiative; encoded archival description (EAD); other applications of…

Migrating an Online Service to WAP - A Case Study.

ERIC Educational Resources Information Center

Klasen, Lars

2002-01-01

Discusses mobile access via wireless application protocol (WAP) to online services that is offered in Sweden through InfoTorg. Topics include the Swedish online market; filtering HTML data from an Internet/Web server into WML (wireless markup language); mobile phone technology; microbrowsers; WAP protocol; and future possibilities. (LRW)

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.

Silicon Graphics' IRIS InSight: An SGML Success Story.

ERIC Educational Resources Information Center

Glushko, Robert J.; Kershner, Ken

1993-01-01

Offers a case history of the development of the Silicon Graphics "IRIS InSight" system, a system for viewing on-line documentation using Standard Generalized Markup Language. Notes that SGML's explicit encoding of structure and separation of structure and presentation make possible structure-based search, alternative structural views of…

Control and the Cyborg: Writing and Being Written in Hypertext.

ERIC Educational Resources Information Center

Johnson-Eilola, Johndan

1993-01-01

Describes the computer technology called hypertext, especially as it relates to teaching composition. Argues that the ability to redistribute textual control hold both empowerment and danger for hypertext writer/readers, who can be compared to cyborgs. Discusses the implications of hypertext for composition pedagogy. (HB)

Empirical Evaluation of Adaptive Annotation in Hypermedia.

ERIC Educational Resources Information Center

Specht, Marcus

Empirical evaluations of learning with hypertext have shown contradictory results. Adaptive hypertext was introduced to solve some problems when learning with hypertext. This paper reports on two empirical studies comparing different forms of adaptive hypertext. In the first experiment, four treatments were realized by a combination of adaptive…

Visual-Spatial Thinking in Hypertexts.

ERIC Educational Resources Information Center

Johnson-Sheehan, Richard; Baehr, Craig

2001-01-01

Explores what it means to think visually and spatially in hypertexts and how users react and maneuver in real and virtual three-dimensional spaces. Offers four principles of visual thinking that can be applied when developing hypertexts. Applies these principles to actual hypertexts, demonstrating how selectivity, fixation, depth discernment, and…

Seven ways to make a hypertext project fail

NASA Technical Reports Server (NTRS)

Glushko, Robert J.

1990-01-01

Hypertext is an exciting concept, but designing and developing hypertext applications of practical scale is hard. To make a project feasible and successful 'hypertext engineers' must overcome the following problems: (1) developing realistic expectations in the face of hypertext hype; (2) assembling a multidisciplinary project team; (3) establishing and following design guidelines; (4) dealing with installed base constraints; (5) obtaining usable source files; (6) finding appropriate software technology and methods; and (7) overcoming legal uncertainties about intellectual property concerns.

A review of hypertext in a NASA project management context

NASA Technical Reports Server (NTRS)

Bell, Christopher J.

1987-01-01

The principles of data storage, the comparative strengths of data bases, and the evolution of hypertext within this context are discussed. A classification schema of indexing and of hypertext document structures is provided. Issues associated with hypertext implementation are also discussed and potential areas for further research are indicated.

The Effectiveness of Instruction-Oriented Hypertext Systems Compared to Direct Instruction in E-Learning Environments

ERIC Educational Resources Information Center

Barhoumi, Chokri; Rossi, Pier Giuseppe

2013-01-01

The use of hypertext systems for learning and teaching complex and ill-structured domain of knowledge has been attracting attention in design of instruction. In this context, an experimental research has been conducted to explore the effectiveness of instructional design oriented hypertext systems. Cognitive flexibility hypertext theory is…

Learner Variables Associated with Reading and Learning in a Hypertext Environment.

ERIC Educational Resources Information Center

Niederhauser, Dale S.; Shapiro, Amy

While many elements like character decoding, word recognition, comprehension, and others remain the same as in learning from traditional text, when learning from hypertext, a number of features that are unique to reading hypertext produce added complexity. It is these features that drive research on hypertext in education. There is a greater…

Semantic Web Services with Web Ontology Language (OWL-S) - Specification of Agent-Services for DARPA Agent Markup Language (DAML)

DTIC Science & Technology

2006-08-01

effective for describing taxonomic categories and properties of things, the structures found in SWRL and SPARQL are better suited to describing conditions...up the query processing time, which may occur many times and furthermore it is time critical. In order to maintain information about the...that time spent during this phase does not depend linearly on the number of concepts present in the data structure , but in the order of log of concepts

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

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

2015-01-01

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

Effects of Different Metaphor Usage on Hypertext Learning

ERIC Educational Resources Information Center

Merdivan, Ece; Ozdener, Nesrin

2011-01-01

There are many studies that offer different opinions on the effects of hypertext usage as an educational tool. Given the differences of opinion, it is useful to research the effects of metaphor usage in hypertext education and the use of hypertext as an educational tool. In this study, the effects of metaphors' uses in constructing the…

36 CFR 1235.50 - What specifications and standards for transfer apply to electronic records?

Code of Federal Regulations, 2012 CFR

2012-07-01

... electronic records in a format that is independent of specific hardware or software. Except as specified in... a request from NARA to provide the software to decompress the records. (3) Agencies interested in... organization. Acceptable transfer formats include the Geography Markup Language (GML) as defined by the Open...

Federated Process Framework in a Virtual Enterprise Using an Object-Oriented Database and Extensible Markup Language.

ERIC Educational Resources Information Center

Bae, Kyoung-Il; Kim, Jung-Hyun; Huh, Soon-Young

2003-01-01

Discusses process information sharing among participating organizations in a virtual enterprise and proposes a federated process framework and system architecture that provide a conceptual design for effective implementation of process information sharing supporting the autonomy and agility of the organizations. Develops the framework using an…

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…

A two-way interface between limited Systems Biology Markup Language and R.

PubMed

Radivoyevitch, Tomas

2004-12-07

Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R. A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML. List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.

PIML: the Pathogen Information Markup Language.

PubMed

He, Yongqun; Vines, Richard R; Wattam, Alice R; Abramochkin, Georgiy V; Dickerman, Allan W; Eckart, J Dana; Sobral, Bruno W S

2005-01-01

A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data. The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents. All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

A two-way interface between limited Systems Biology Markup Language and R

PubMed Central

Radivoyevitch, Tomas

2004-01-01

Background Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R. Results A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML. Conclusions List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted. PMID:15585059

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages.

PubMed

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia.

Learning Asset Technology Integration Support Tool Design Document

DTIC Science & Technology

2010-05-11

language known as Hypertext Preprocessor ( PHP ) and by MySQL – a relational database management system that can also be used for content management. It...Requirements The LATIST tool will be implemented utilizing a WordPress platform with MySQL as the database. Also the LATIST system must effectively work... MySQL . When designing the LATIST system there are several considerations which must be accounted for in the working prototype. These include: • DAU

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

PubMed Central

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

2013-01-01

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

Dealing with Diversity in Computational Cancer Modeling

PubMed Central

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

2013-01-01

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

Education and Training Module in Alertness Management

NASA Technical Reports Server (NTRS)

Mallis, M. M.; Brandt, S. L.; Oyung, R. L.; Reduta, D. D.; Rosekind, M. R.

2006-01-01

The education and training module (ETM) in alertness management has now been integrated as part of the training regimen of the Pilot Proficiency Awards Program ("WINGS") of the Federal Aviation Administration. Originated and now maintained current by the Fatigue Countermeasures Group at NASA Ames Research Center, the ETM in Alertness Management is designed to give pilots the benefit of the best and most recent research on the basics of sleep physiology, the causes of fatigue, and strategies for managing alertness during flight operations. The WINGS program is an incentive program that encourages pilots at all licensing levels to participate in recurrent training, upon completion of which distinctive lapel or tie pins (wings) and certificates of completion are awarded. In addition to flight training, all WINGS applicants must attend at least one FAA-sponsored safety seminar, FAA-sanctioned safety seminar, or industry recurrent training program. The Fatigue Countermeasures Group provides an FAA-approved industry recurrent training program through an on-line General Aviation (GA) WINGS ETM in alertness management to satisfy this requirement. Since 1993, the Fatigue Countermeasures Group has translated fatigue and alertness information to operational environments by conducting two-day ETM workshops oriented primarily toward air-carrier operations subject to Part 121 of the Federal Aviation Regulations pertaining to such operations. On the basis of the information presented in the two-day ETM workshops, an ETM was created for GA pilots and was transferred to a Web-based version. To comply with the requirements of the WINGS Program, the original Web-based version has been modified to include hypertext markup language (HTML) content that makes information easily accessible, in-depth testing of alertness-management knowledge, new interactive features, and increased informational resources for GA pilots. Upon successful completion of this training module, a participant receives a computer- screen display of a certificate of completion. The certificate, which includes the pilot s name and an identifying number, can be printed out and submitted, for ground training credit, with the pilot s WINGS application.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

A Courseware to Script Animated Pedagogical Agents in Instructional Material for Elementary Students in English Education

ERIC Educational Resources Information Center

Hong, Zeng-Wei; Chen, Yen-Lin; Lan, Chien-Ho

2014-01-01

Animated agents are virtual characters who demonstrate facial expressions, gestures, movements, and speech to facilitate students' engagement in the learning environment. Our research developed a courseware that supports a XML-based markup language and an authoring tool for teachers to script animated pedagogical agents in teaching materials. The…

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

Gear Up Your Research Guides with the Emerging OPML Codes

ERIC Educational Resources Information Center

Wilcox, Kimberley

2006-01-01

Outline Processor Markup Language (OPML) is an emerging format that allows for the creation of customized research packages to push to patrons. It is a way to gather collections of Web resources (links, RSS feeds, multimedia files), organize them as outlines, and publish them in a format that others can share and even subscribe to. In this…

Query by Browsing: An Alternative Hypertext Information Retrieval Method

PubMed Central

Frisse, Mark E.; Cousins, Steve B.

1989-01-01

In this paper we discuss our efforts to develop programs which enhance the ability to navigate through large medical hypertext systems. Our approach organizes hypertext index terms into a belief network and uses reader feedback to update the degree of belief in the index terms' utility to a query. We begin by describing various possible configurations for indexes to hypertext. We then describe how belief network calculations can be applied to these indexes. After a brief discussion of early results using manuscripts from a medical handbook, we close with an analysis of our approach's applicability to a wider range of hypertext information retrieval problems.

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages

PubMed Central

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia. PMID:24266292

Integrated Reconfigurable Intelligent Systems (IRIS) for Complex Naval Systems

DTIC Science & Technology

2009-10-31

water system. This simplified chilled water system includes one chiller -pump plant and two service loads. • X- p«cM*MJ<w*4tf -a ’.•.wVlniX’i • V...and valve7. Pumps and chiller operation states are observable. Valve 7 is STUCKCLOSE at time / = 440sec (me 11th iteration). Valve 11 is STUCKCLOSE...framework is a product from Adobe called Flex. The product is a mixture of the Adobe Action script programming language and a markup language call MXML

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

PubMed

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

2008-03-01

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

Future perspectives - proposal for Oxford Physiome Project.

PubMed

Oku, Yoshitaka

2010-01-01

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

Post-Nor'Ida coastal oblique aerial photographs collected from Ocean City, Maryland, to Hatteras, North Carolina, December 4, 2009

USGS Publications Warehouse

Morgan, Karen L. M.; Krohn, M. Dennis; Guy, Kristy K.

2015-01-01

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

Baseline Coastal Oblique Aerial Photographs Collected from Navarre Beach, Florida, to Breton Island, Louisiana, September 1, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-08-31

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

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

ERIC Educational Resources Information Center

Herrera-Viedma, Enrique; Peis, Eduardo

2003-01-01

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

Automatic Configuration of Programmable Logic Controller Emulators

DTIC Science & Technology

2015-03-01

25 11 Example tree generated using UPGMA [Edw13] . . . . . . . . . . . . . . . . . . . . 33 12 Example sequence alignment for two... UPGMA Unweighted Pair Group Method with Arithmetic Mean URL uniform resource locator VM virtual machine XML Extensible Markup Language xx List of...appearance in the ses- sion, and then they are clustered again using Unweighted Pair Group Method with Arithmetic Mean ( UPGMA ) with a distance matrix based

Gopher Is No Longer Just a Rodent: Using Gopher and World Wide Web in Composition Studies.

ERIC Educational Resources Information Center

Krause, Steve

Gopher and World Wide Web (WWW) are two useful Internet technologies for the composition and rhetoric classroom. Gopher software makes available a wide variety of text-based information in the Internet. A Gopher at Bowling Green State University offers many types of information. The World Wide Web, using a fairly simple markup language, is also…

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

ERIC Educational Resources Information Center

Merrill, Paul F.

2005-01-01

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

The 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

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.

Using XML and Java for Astronomical Instrumentation Control

NASA Technical Reports Server (NTRS)

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

2000-01-01

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

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

PubMed

Watanabe, Leandro; Myers, Chris J

2016-08-19

The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime.

A methodology to annotate systems biology markup language models with the synthetic biology open language.

PubMed

Roehner, Nicholas; Myers, Chris J

2014-02-21

Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

Application of World Wide Web (W3) Technologies in Payload Operations

NASA Technical Reports Server (NTRS)

Sun, Charles; Windrem, May; Picinich, Lou

1996-01-01

World Wide Web (W3) technologies are considered in relation to their application to space missions. It is considered that such technologies, including the hypertext transfer protocol and the Java object-oriented language, offer a powerful and relatively inexpensive framework for distributed application software development. The suitability of these technologies for payload monitoring systems development is discussed, and the experience gained from the development of an insect habitat monitoring system based on W3 technologies is reported.

Misleading Theoretical Assumptions in Hypertext/Hypermedia Research.

ERIC Educational Resources Information Center

Tergan, Sigmar-Olaf

1997-01-01

Reviews basic theoretical assumptions of research on learning with hypertext/hypermedia. Focuses on whether the results of research on hypertext/hypermedia-based learning support these assumptions. Results of empirical studies and theoretical analysis reveal that many research approaches have been misled by inappropriate theoretical assumptions on…

Hypertext Interchange Using ICA.

ERIC Educational Resources Information Center

Rada, Roy; And Others

1995-01-01

Discusses extended ICA (Integrated Chameleon Architecture), a public domain toolset for generating text-to-hypertext translators. A system called SGML-MUCH has been developed using E-ICA (Extended Integrated Chameleon Architecture) and is presented as a case study with converters for the hypertext systems MUCH, Guide, Hyperties, and Toolbook.…

What's New in Software? Hot New Tool: The Hypertext.

ERIC Educational Resources Information Center

Hedley, Carolyn N.

1989-01-01

This article surveys recent developments in hypertext software, a highly interactive nonsequential reading/writing/database approach to research and teaching that allows paths to be created through related materials including text, graphics, video, and animation sources. Described are uses, advantages, and problems of hypertext. (PB)

Cognitive Overhead in Hypertext Learning Reexamined: Overcoming the Myths

ERIC Educational Resources Information Center

Zumbach, Joerg

2006-01-01

In hypertext learning, comparative research is mostly dedicated to differences in text-hypertext information retrieval and processing and to optimization of nonlinear information retrieval. Most of these investigations are conducted within the context of applied research. The theoretical background of information acquisition from linear and…

Conceptual and Methodological Shortcomings in Hypertext/Hypermedia Design and Research.

ERIC Educational Resources Information Center

Tergan, Sigmar-Olaf

1997-01-01

Some studies of hypertext/hypermedia systems have concluded that there is little evidence supporting its educational efficacy. After examining conceptual and methodological shortcomings of research, this article suggests that the educational potential of hypertext/hypermedia has been underestimated and argues that overcoming these shortcomings…

FuGEFlow: data model and markup language for flow cytometry.

PubMed

Qian, Yu; Tchuvatkina, Olga; Spidlen, Josef; Wilkinson, Peter; Gasparetto, Maura; Jones, Andrew R; Manion, Frank J; Scheuermann, Richard H; Sekaly, Rafick-Pierre; Brinkman, Ryan R

2009-06-16

Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description. The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project. We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.

The User Interface: A Hypertext Model Linking Art Objects and Related Information.

ERIC Educational Resources Information Center

Moline, Judi

This report presents a model combining the emerging technologies of hypertext and expert systems. Hypertext is relatively unexplored but promises an innovative approach to information retrieval. In contrast, expert systems have been used experimentally in many different application areas ranging from medical diagnosis to oil exploration. The…

Hypertext Publishing and the Revitalization of Knowledge.

ERIC Educational Resources Information Center

Louie, Steven; Rubeck, Robert F.

1989-01-01

Discusses the use of hypertext for publishing and other document control activities in higher education. Topics discussed include a model of hypertext, called GUIDE, that is used at the University of Arizona Medical School; the increase in the number of scholarly publications; courseware development by faculty; and artificial intelligence. (LRW)

Hypertext: Behind the Hype. ERIC Digest.

ERIC Educational Resources Information Center

Bevilacqua, Ann F.

This digest begins by defining the concept of hypertext and describing the two types of hypertext--static and dynamic. Three prototype applications are then discussed: (1) Intermedia, a large-scale multimedia system at Brown University; (2) the Perseus Project at Harvard University, which is developing interactive courseware on classical Greek…

Baseline coastal oblique aerial photographs collected from the Virginia/North Carolina border to Montauk Point, New York, October 5-6, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-10-02

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

SSO - Single-Sign-On Profile: Authentication Mechanisms Version 2.0

NASA Astrophysics Data System (ADS)

Taffoni, Giuliano; Schaaf, André; Rixon, Guy; Major, Brian; Taffoni, Giuliano

2017-05-01

Approved client-server authentication mechanisms are described for the IVOA single-sign-on profile: No Authentication; HTTP Basic Authentication; TLS with passwords; TLS with client certificates; Cookies; Open Authentication; Security Assertion Markup Language; OpenID. Normative rules are given for the implementation of these mechanisms, mainly by reference to pre-existing standards. The Authorization mechanisms are out of the scope of this document.

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.

Consolidated Environmental Resource Database Information Process (CERDIP)

DTIC Science & Technology

2015-11-19

Secretary of the Army for Installations, Energy and Environment [OASA(IE&E)] ESOH 5850 21st Street, Bldg 211, Second Floor Fort Belvoir, VA 22060-5938...Elizabeth J. Keysar 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) National Defense Center for Energy and Environment Operated by Concurrent...Markup Language NDCEE National Defense Center for Energy and Environment NFDD National Geospatial–Intelligence Agency Feature Data Dictionary

Meditations upon Hypertext: A Rhetorethics for Cyborgs.

ERIC Educational Resources Information Center

Gilbert, Pamela K.

1997-01-01

Suggests that the ability to actualize the potential of hypertext is limited by the lack of an adequate theory of hypertext reading which accounts for ethical and political issues of identity or subjectivity. Identifies examples of this problem and speculates on some responses; considers what sort of reader and/or reading practices hypertext…

Navigation and Comprehension of Digital Expository Texts: Hypertext Structure, Previous Domain Knowledge, and Working Memory Capacity

ERIC Educational Resources Information Center

Burin, Debora I.; Barreyro, Juan P.; Saux, Gastón; Irrazábal, Natalia C.

2015-01-01

Introduction: In contemporary information societies, reading digital text has become pervasive. One of the most distinctive features of digital texts is their internal connections via hyperlinks, resulting in non-linear hypertexts. Hypertext structure and previous knowledge affect navigation and comprehension of digital expository texts. From the…

Using an Architectural Metaphor for Information Design in Hypertext.

ERIC Educational Resources Information Center

Deboard, Donn R.; Lee, Doris

2001-01-01

Uses Frank Lloyd Wright's (1867-1959) organic architecture as a metaphor to define the relationship between a part and a whole, whether the focus is on a building and its surroundings or information delivered via hypertext. Reviews effective strategies for designing text information via hypertext and incorporates three levels of information…

Techniques for capturing expert knowledge - An expert systems/hypertext approach

NASA Technical Reports Server (NTRS)

Lafferty, Larry; Taylor, Greg; Schumann, Robin; Evans, Randy; Koller, Albert M., Jr.

1990-01-01

The knowledge-acquisition strategy developed for the Explosive Hazards Classification (EHC) Expert System is described in which expert systems and hypertext are combined, and broad applications are proposed. The EHC expert system is based on rapid prototyping in which primary knowledge acquisition from experts is not emphasized; the explosive hazards technical bulletin, technical guidance, and minimal interviewing are used to develop the knowledge-based system. Hypertext is used to capture the technical information with respect to four issues including procedural, materials, test, and classification issues. The hypertext display allows the integration of multiple knowlege representations such as clarifications or opinions, and thereby allows the performance of a broad range of tasks on a single machine. Among other recommendations, it is suggested that the integration of hypertext and expert systems makes the resulting synergistic system highly efficient.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

PubMed

Kell, Douglas B; Mendes, Pedro

2008-06-07

Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization.

Modeling the Arden Syntax for medical decisions in XML.

PubMed

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

2008-10-01

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

Linking Information to Objects: A Hypertext Prototype for Numismatists.

ERIC Educational Resources Information Center

Moline, Judi

1991-01-01

This report focuses on the user of a prototype hypertext application designed to help coin collectors link ancient coins with relevant numismatic information. It is noted that hypertext systems promote the collection of information that may be multimedia in nature and may be linked so that information can be accessed in a non-linear manner. The…

Extended Subject Access to Hypertext Online Documentation. Parts I and II: The Search-Support and Maintenance Problems.

ERIC Educational Resources Information Center

Girill, T. R.; And Others

1991-01-01

Describes enhancements made to a hypertext information retrieval system at the National Energy Research Supercomputer Center (NERSC) called DFT (Document, Find, and Theseus). The enrichment of DFT's entry vocabulary is described, DFT and other hypertext systems are compared, and problems that occur due to the need for frequent updates are…

Creating and Evaluating a Hypertext System of Documenting Analytical Test Methods in a Chemical Plant Quality Assurance Laboratory.

ERIC Educational Resources Information Center

White, Charles E., Jr.

The purpose of this study was to develop and implement a hypertext documentation system in an industrial laboratory and to evaluate its usefulness by participative observation and a questionnaire. Existing word-processing test method documentation was converted directly into a hypertext format or "hyperdocument." The hyperdocument was designed and…

Proceedings of the Hypertext Standardization Workshop (Gaithersburg, Maryland, January 16-18, 1990).

ERIC Educational Resources Information Center

Moline, Judi, Ed.; And Others

This report constitutes the proceedings of a three day workshop on Hypertext Standardization held at the National Institute of Standards and Technology (NIST) on January 16-18, 1990. Efforts towards standardization of hypertext have already been initiated in various interested organizations. The major purpose of the workshop was to provide a forum…

Hypertext and Hypermedia: Applications for Educational Use. Year 2 Monograph.

ERIC Educational Resources Information Center

Boone, Randall; Higgins, Kyle

This report presents information on the second year of a 3-year project to develop hypertext computer study guides and to study their use by secondary students, including remedial students and those with learning disabilities. The first section provides an introduction to hypertext, what it is, how it is structured, and how it compares with…

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Hospital markup and operation outcomes in the United States.

PubMed

Gani, Faiz; Ejaz, Aslam; Makary, Martin A; Pawlik, Timothy M

2016-07-01

Although the price hospitals charge for operations has broad financial implications, hospital pricing is not subject to regulation. We sought to characterize national variation in hospital price markup for major cardiothoracic and gastrointestinal operations and to evaluate perioperative outcomes of hospitals relative to hospital price markup. All hospitals in which a patient underwent a cardiothoracic or gastrointestinal procedure were identified using the Nationwide Inpatient Sample for 2012. Markup ratios (ratio of charges to costs) for the total cost of hospitalization were compared across hospitals. Risk-adjusted morbidity, failure-to-rescue, and mortality were calculated using multivariable, hierarchical logistic regression. Among the 3,498 hospitals identified, markup ratios ranged from 0.5-12.2, with a median markup ratio of 2.8 (interquartile range 2.7-3.9). For the 888 hospitals with extreme markup (greatest markup ratio quartile: markup ratio >3.9), the median markup ratio was 4.9 (interquartile range 4.3-6.0), with 10% of these hospitals billing more than 7 times the Medicare-allowable costs (markup ratio ≥7.25). Extreme markup hospitals were more often large (46.3% vs 33.8%, P < .001), urban, nonteaching centers (57.0% vs 37.9%, P < .001), and located in the Southern (46.4% vs 32.8%, P < .001) or Western (27.8% vs 17.6%, P < .001) regions of the United States. Of the 639 investor-owned, for-profit hospitals, 401 hospitals (62.8%) had an extreme markup ratio compared with 19.3% (n = 452) and 6.8% (n = 35) of nonprofit and government hospitals, respectively. Perioperative morbidity (32.7% vs 26.4%, P < .001) was greater at extreme markup hospitals. There is wide variation in hospital markup for cardiothoracic and gastrointestinal procedures, with approximately a quarter of hospital charges being 4 times greater than the actual cost of hospitalization. Hospitals with an extreme markup had greater perioperative morbidity. Copyright © 2016 Elsevier Inc. All rights reserved.

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…

Baseline coastal oblique aerial photographs collected from Navarre Beach, Florida, to Breton Island, Louisiana, September 18–19, 2015

USGS Publications Warehouse

Morgan, Karen L. M.

2016-08-01

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then the thumbnail or the link below the thumbnail. The KML file was created using the photographic navigation files. This KML file can be found in the kml folder.

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.

CellML and associated tools and techniques.

PubMed

Garny, Alan; Nickerson, David P; Cooper, Jonathan; Weber dos Santos, Rodrigo; Miller, Andrew K; McKeever, Steve; Nielsen, Poul M F; Hunter, Peter J

2008-09-13

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results. The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

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.

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

PubMed

Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

2015-12-01

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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

PubMed

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

2001-01-01

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

Hypertext Theory: Rethinking and Reformulating What We Know, Web 2.0

ERIC Educational Resources Information Center

Baehr, Craig; Lang, Susan M.

2012-01-01

This article traces the influences of hypertext theory throughout the various genres of online publication in technical communication. It begins with a look back at some of the important concepts and theorists writing about hypertext theory from the post-World War II era, to the early years of the World Wide Web 2.0, and the very differing notions…

Development of an intelligent hypertext system for wind tunnel testing

NASA Technical Reports Server (NTRS)

Lo, Ching F.; Shi, George Z.; Steinle, Frank W.; Wu, Y. C. L. Susan; Hoyt, W. Andes

1991-01-01

This paper summarizes the results of a system utilizing artificial intelligence technology to improve the productivity of project engineers who conduct wind tunnel tests. The objective was to create an intelligent hypertext system which integrates a hypertext manual and expert system that stores experts' knowledge and experience. The preliminary (Phase I) effort implemented a prototype IHS module encompassing a portion of the manuals and knowledge used for wind tunnel testing. The effort successfully demonstrated the feasibility of the intelligent hypertext system concept. A module for the internal strain gage balance, implemented on both IBM-PC and Macintosh computers, is presented. A description of the Phase II effort is included.

Toward intelligent information sysytem

NASA Astrophysics Data System (ADS)

Onodera, Natsuo

"Hypertext" means a concept of a novel computer-assisted tool for storage and retrieval of text information based on human association. Structure of knowledge in our idea processing is generally complicated and networked, but traditional paper documents merely express it in essentially linear and sequential forms. However, recent advances in work-station technology have allowed us to process easily electronic documents containing non-linear structure such as references or hierarchies. This paper describes concept, history and basic organization of hypertext, and shows the outline and features of existing main hypertext systems. Particularly, use of the hypertext database is illustrated by an example of Intermedia developed by Brown University.

Goal-Directed Reading of Complex, Embedded Hypertexts: Effects of Goal and Interest on Search Strategies and Selective Attention.

ERIC Educational Resources Information Center

Gillingham, Mark G.

A study examined what happened when a group of adult students read a hypertext for the goal of answering specific questions. Subjects, 30 students enrolled in an upper-division psychology course at a state university in the northwestern United States, read a binary tree-structured hypertext to answer three two-part questions on the topic of…

Moves in Hypertext: The Resource of Negotiation as a Means to Describe the Way Students Navigate a Pathway through Hypertext

ERIC Educational Resources Information Center

Zammit, Katina

2011-01-01

With the increased use of hypertexts to locate information, students need to make informed decisions about their pathway so they build knowledge efficiently. The moves they make need to contribute to understanding the topic more than detracting them. This paper explores the use of Systemic Functional Linguistics (SFL) to describe the construction…

FuGEFlow: data model and markup language for flow cytometry

PubMed Central

Qian, Yu; Tchuvatkina, Olga; Spidlen, Josef; Wilkinson, Peter; Gasparetto, Maura; Jones, Andrew R; Manion, Frank J; Scheuermann, Richard H; Sekaly, Rafick-Pierre; Brinkman, Ryan R

2009-01-01

Background Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. Methods We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description. Results The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project. Conclusion We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development. PMID:19531228

ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

PubMed

Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

2013-01-01

With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software models. ART-ML can be used as a reference ML model in multiscale simulations of plaque formation and progression, incorporating all scales of the biological processes.

Baseline coastal oblique aerial photographs collected from Key Largo, Florida, to the Florida/Georgia border, September 5-6, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-09-14

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files. These KML files can be found in the kml folder.

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

DTIC Science & Technology

2008-03-01

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

An Approach to Dynamic Service Management in Pervasive Computing Systems

DTIC Science & Technology

2005-01-01

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

XML Schema Guide for Primary CDR Submissions

EPA Pesticide Factsheets

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

Expanding the Toolkit and Resource Environment to Assist Translation (TREAT) and Its User Base

DTIC Science & Technology

2011-06-01

3 Figure 2. Screenshot of TREAT (translation of Arabic source into English target) and two corresponding markup tool windows on Arabic source...initial framework in place, we decided to expand TREAT to provide support to two new groups of users: students learning to be Arabic -language...translators and teachers training them. The students and the teachers are native English speakers, so the training includes learning how to read Arabic

Semantic message oriented middleware for publish/subscribe networks

NASA Astrophysics Data System (ADS)

Li, Han; Jiang, Guofei

2004-09-01

The publish/subscribe paradigm of Message Oriented Middleware provides a loosely coupled communication model between distributed applications. Traditional publish/subscribe middleware uses keywords to match advertisements and subscriptions and does not support deep semantic matching. To this end, we designed and implemented a Semantic Message Oriented Middleware system to provide such capabilities for semantic description and matching. We adopted the DARPA Agent Markup Language and Ontology Inference Layer, a formal knowledge representation language for expressing sophisticated classifications and enabling automated inference, as the topic description language in our middleware system. A simple description logic inference system was implemented to handle the matching process between the subscriptions of subscribers and the advertisements of publishers. Moreover our middleware system also has a security architecture to support secure communication and user privilege control.

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank T

2015-06-01

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank Thomas

2015-09-04

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

WebWatcher: Machine Learning and Hypertext

DTIC Science & Technology

1995-05-29

WebWatcher: Machine Learning and Hypertext Thorsten Joachims, Tom Mitchell, Dayne Freitag, and Robert Armstrong School of Computer Science Carnegie...HTML-page about machine learning in which we in- serted a hyperlink to WebWatcher (line 6). The user follows this hyperlink and gets to a page which...AND SUBTITLE WebWatcher: Machine Learning and Hypertext 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT

How to Assess Data Availability, Accessibility and Format for Risk Analysis?

PubMed

Humblet, M-F; Vandeputte, S; Mignot, C; Bellet, C; De Koeijer, A; Swanenburg, M; Afonso, A; Sanaa, M; Saegerman, C

2016-12-01

Risk assessments are mostly carried out based on available data, which do not reflect all data theoretically required by experts to answer them. This study aimed at developing a methodology to assess data availability, accessibility and format, based on a scoring system and focusing on two diseases: Venezuelan equine encephalomyelitis (VEE), still exotic to Europe, and alveolar echinococcosis, caused by Echinococcus multilocularis (EM), endemic in several Member States (MSs). After reviewing 36 opinions of the EFSA-AHAW Panel on risk assessment of animal health questions, a generic list of needed data was elaborated. The methodology consisted, first, in implementing a direct and an indirect survey to collect the data needed for both case studies: the direct survey consisted in a questionnaire sent to contact points of three European MSs (Belgium, France and the Netherlands), and the organization of a workshop gathering experts on both diseases. The indirect survey, focusing on the three MSs involved in the direct survey plus Spain, relied on web searches. Secondly, a scoring system with reference to data availability, accessibility and format was elaborated, to, finally, compare both diseases and data between MSs. The accessibility of data was generally related to their availability. Web searches resulted in more data available for VEE compared to EM, despite its current exotic status in the European Union. Hypertext markup language and portable document files were the main formats of available data. Data availability, accessibility and format should be improved for research scientists/assessors. The format of data plays a key role in the feasibility and rapidness of data management and analysis, through a prompt compilation, combination and aggregation in working databases. Harmonization of data collection process is encouraged, according to standardized procedures, to provide useful and reliable data, both at the national and the international levels for both animal and human health; it would allow assessing data gaps through comparative studies. The present methodology is a good way of assessing the relevance of data for risk assessment, as it allows integrating the uncertainty linked to the quality of data used. Such an approach could be described as transparent and traceable and should be performed systematically. © 2015 Blackwell Verlag GmbH.

National Authentication Framework Implementation Study

DTIC Science & Technology

2009-12-01

Identifiers RA Registration Authority SAML Security Assertion Markup Language SFA Single-factor Authentication SMS Short Messaging System SOA ...written on  paper  disclosed;  passwords stored in electronic file  copied. 1,2,3,4 Eaves‐  dropping The token secret or authenticator is  revealed to...Internet 2.0 and the growing interest in systems developed based upon the Service- Oriented Architecture ( SOA ). While core specifications upon which

Network Application Server Using Extensible Mark-Up Language (XML) to Support Distributed Databases and 3D Environments

DTIC Science & Technology

2001-12-01

diides.ncr.disa.mil/xmlreg/user/index.cfm] [ Deitel ] Deitel , H., Deitel , P., Java How to Program 3rd Edition, Prentice Hall, 1999. [DL99...presentation, and data) of information and the programming functionality. The Web framework addressed ability to provide a framework for the distribution...BLANK v ABSTRACT Advances in computer communication technology and an increased awareness of how enhanced information access can lead to improved

XML Schema Guide for Secondary CDR Submissions

EPA Pesticide Factsheets

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

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. \

Internet Economics IV

DTIC Science & Technology

2004-08-01

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

Operational Monitoring of Volcanoes Using Keyhole Markup Language

NASA Astrophysics Data System (ADS)

Dehn, J.; Bailey, J. E.; Webley, P.

2007-12-01

Volcanoes are some of the most geologically powerful, dynamic, visually appealing structures on the Earth's landscape. Volcanic eruptions are hard to predict, difficult to quantify and impossible to prevent, making effective monitoring a difficult proposition. In Alaska, volcanoes are an intrinsic part of the culture, with over 100 volcanoes and volcanic fields that have been active in historic time monitored by the Alaska Volcano Observatory (AVO). Observations and research are performed using a suite of methods and tools in the fields of remote sensing, seismology, geodesy and geology, producing large volumes of geospatial data. Keyhole Markup Language (KML) offers a context in which these different, and in the past disparate, data can be displayed simultaneously. Dynamic links keep these data current, allowing it to be used in an operational capacity. KML is used to display information from the aviation color codes and activity alert levels for volcanoes to locations of thermal anomalies, earthquake locations and ash plume modeling. The dynamic refresh and time primitive are used to display volcano webcam and satellite image overlays in near real-time. In addition a virtual globe browser using KML, such as Google Earth, provides an interface to further information using the hyperlink, rich- text and flash-embedding abilities supported within object description balloons. By merging these data sets in an easy to use interface, a virtual globe browser provides a better tool for scientists and emergency managers alike to mitigate volcanic crises.

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.

Balancing medicine prices and business sustainability: analyses of pharmacy costs, revenues and profit shed light on retail medicine mark-ups in rural Kyrgyzstan

PubMed Central

2010-01-01

Background Numerous not-for-profit pharmacies have been created to improve access to medicines for the poor, but many have failed due to insufficient financial planning and management. These pharmacies are not well described in health services literature despite strong demand from policy makers, implementers, and researchers. Surveys reporting unaffordable medicine prices and high mark-ups have spurred efforts to reduce medicine prices, but price reduction goals are arbitrary in the absence of information on pharmacy costs, revenues, and profit structures. Health services research is needed to develop sustainable and "reasonable" medicine price goals and strategic initiatives to reach them. Methods We utilized cost accounting methods on inventory and financial information obtained from a not-for-profit rural pharmacy network in mountainous Kyrgyzstan to quantify costs, revenues, profits and medicine mark-ups during establishment and maintenance periods (October 2004-December 2007). Results Twelve pharmacies and one warehouse were established in remote Kyrgyzstan with < US $25,000 due to governmental resource-sharing. The network operated at break-even profit, leaving little room to lower medicine prices and mark-ups. Medicine mark-ups needed for sustainability were greater than originally envisioned by network administration. In 2005, 55%, 35%, and 10% of the network's top 50 products revealed mark-ups of < 50%, 50-99% and > 100%, respectively. Annual mark-ups increased dramatically each year to cover increasing recurrent costs, and by 2007, only 19% and 46% of products revealed mark-ups of < 50% and 50-99%, respectively; while 35% of products revealed mark-ups > 100%. 2007 medicine mark-ups varied substantially across these products, ranging from 32% to 244%. Mark-ups needed to sustain private pharmacies would be even higher in the absence of government subsidies. Conclusion Pharmacy networks can be established in hard-to-reach regions with little funding using public-private partnership, resource-sharing models. Medicine prices and mark-ups must be interpreted with consideration for regional costs of business. Mark-ups vary dramatically across medicines. Some mark-ups appear "excessive" but are likely necessary for pharmacy viability. Pharmacy financial data is available in remote settings and can be used towards determination of "reasonable" medicine price goals. Health systems researchers must document the positive and negative financial experiences of pharmacy initiatives to inform future projects and advance access to medicines goals. PMID:20626904

Balancing medicine prices and business sustainability: analyses of pharmacy costs, revenues and profit shed light on retail medicine mark-ups in rural Kyrgyzstan.

PubMed

Waning, Brenda; Maddix, Jason; Soucy, Lyne

2010-07-13

Numerous not-for-profit pharmacies have been created to improve access to medicines for the poor, but many have failed due to insufficient financial planning and management. These pharmacies are not well described in health services literature despite strong demand from policy makers, implementers, and researchers. Surveys reporting unaffordable medicine prices and high mark-ups have spurred efforts to reduce medicine prices, but price reduction goals are arbitrary in the absence of information on pharmacy costs, revenues, and profit structures. Health services research is needed to develop sustainable and "reasonable" medicine price goals and strategic initiatives to reach them. We utilized cost accounting methods on inventory and financial information obtained from a not-for-profit rural pharmacy network in mountainous Kyrgyzstan to quantify costs, revenues, profits and medicine mark-ups during establishment and maintenance periods (October 2004-December 2007). Twelve pharmacies and one warehouse were established in remote Kyrgyzstan with < US $25,000 due to governmental resource-sharing. The network operated at break-even profit, leaving little room to lower medicine prices and mark-ups. Medicine mark-ups needed for sustainability were greater than originally envisioned by network administration. In 2005, 55%, 35%, and 10% of the network's top 50 products revealed mark-ups of < 50%, 50-99% and > 100%, respectively. Annual mark-ups increased dramatically each year to cover increasing recurrent costs, and by 2007, only 19% and 46% of products revealed mark-ups of < 50% and 50-99%, respectively; while 35% of products revealed mark-ups > 100%. 2007 medicine mark-ups varied substantially across these products, ranging from 32% to 244%. Mark-ups needed to sustain private pharmacies would be even higher in the absence of government subsidies. Pharmacy networks can be established in hard-to-reach regions with little funding using public-private partnership, resource-sharing models. Medicine prices and mark-ups must be interpreted with consideration for regional costs of business. Mark-ups vary dramatically across medicines. Some mark-ups appear "excessive" but are likely necessary for pharmacy viability. Pharmacy financial data is available in remote settings and can be used towards determination of "reasonable" medicine price goals. Health systems researchers must document the positive and negative financial experiences of pharmacy initiatives to inform future projects and advance access to medicines goals.

The use of geospatial web services for exchanging utilities data

NASA Astrophysics Data System (ADS)

Kuczyńska, Joanna

2013-04-01

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

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

Defense Advanced Research Projects Agency (DARPA) Agent Markup Language Computer Aided Knowledge Acquisition

DTIC Science & Technology

2005-06-01

34> <rdfs:subClassOf rdf:resource="#Condition"/> <rdfs:label>Economic Self -Sufficiency Class</rdfs:label> <cnd:categoryCode>C</cnd:categoryCode...cnd:index>3.3.4.1</cnd:index> <cnd:title>Economic Self -Sufficiency</cnd:title> <cnd:definition>The ability of a nation to...34#International_Economic_Position"/> <cnd:subCategory rdf:resource="# Self -Sufficiency_In_Food"/> <cnd:subCategory rdf:resource="# Self

The Air Force Records Management Program: A Paradigm Shift from Compliance to Guiding Principles in an Ever-Changing Information Environment

DTIC Science & Technology

2014-06-22

GIG Global Information Grid GOTS Government Off-the-Shelf HTML Hyper Text Markup Language ICT Information and Communication Technology IEC...maintenance, retrieval, and preservation of vital information created in public and private organizations in all sectors of the economy . It is also the...constructed in the 1940’s, as part of a government-effort to provide employment 120 during the Depression, and boost the economy . This road is set in

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

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

Semantically Enriched Data Access Policies in eHealth.

PubMed

Drozdowicz, Michał; Ganzha, Maria; Paprzycki, Marcin

2016-11-01

Internet of Things (IoT) requires novel solutions to facilitate autonomous, though controlled, resource access. Access policies have to facilitate interactions between heterogeneous entities (devices and humans). Here, we focus our attention on access control in eHealth. We propose an approach based on enriching policies, based on well-known and widely-used eXtensible Access Control Markup Language, with semantics. In the paper we describe an implementation of a Policy Information Point integrated with the HL7 Security and Privacy Ontology.

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Development of Semantic Web - Markup Languages, Web Services, Rules, Explanation, Querying, Proof and Reasoning

DTIC Science & Technology

2008-07-01

Study. WWW2006 Workshop on the Models of Trust for the Web (MTW󈧊), Edinburgh, Scotland, May 22, 2006. • Daniel J. Weitzner, Hal Abelson, Tim Berners ...McGuinness gave an invited talk on ontologies in Intel’s Semantic web day. Other invited speakers were Hendler and Berners - Lee . February 4, 2002...Burke (DARPA) concerning ontology tools. July 19-20, 2000. McGuinness met with W3C representatives ( Berners - Lee , Connolly, Lassila) and other

Intelligent hypertext systems for aerospace engineering applications

NASA Technical Reports Server (NTRS)

Lo, Ching F.

1989-01-01

This paper is a progress report on the utilization of AI technology for assisting users locating and understanding technical information in manuals used for planning and conducting wind tunnel test. The specific goal is to create an Intelligent Hypertext System (IHS) for wind tunnel testing which combines the computerized manual in the form of hypertext and an advisory system that stores experts' knowledge and experiences. A prototype IHS for conducting transonic wind tunnel testing has been constructed with limited knowledge base. The prototype is being evaluated by potential users.

A mobile information management system used in textile enterprises

NASA Astrophysics Data System (ADS)

Huang, C.-R.; Yu, W.-D.

2008-02-01

The mobile information management system (MIMS) for textile enterprises is based on Microsoft Visual Studios. NET2003 Server, Microsoft SQL Server 2000, C++ language and wireless application protocol (WAP) and wireless markup language (WML) technology. The portable MIMS is composed of three-layer structures, i.e. showing layer; operating layer; and data visiting layer corresponding to the port-link module; processing module; and database module. By using the MIMS, not only the information exchanges become more convenient and easier, but also the compatible between the giant information capacity and a micro-cell phone and functional expansion nature in operating and designing can be realized by means of build-in units. The development of MIMS is suitable for the utilization in textile enterprises.

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.

Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information.

PubMed

Gagl, Benjamin

2016-01-01

Highlighted text in the Internet (i.e., hypertext) is predominantly blue and underlined. The perceptibility of these hypertext characteristics was heavily questioned by applied research and empirical tests resulted in inconclusive results. The ability to recognize blue text in foveal and parafoveal vision was identified as potentially constrained by the low number of foveally centered blue light sensitive retinal cells. The present study investigates if foveal and parafoveal perceptibility of blue hypertext is reduced in comparison to normal black text during reading. A silent-sentence reading study with simultaneous eye movement recordings and the invisible boundary paradigm, which allows the investigation of foveal and parafoveal perceptibility, separately, was realized (comparing fixation times after degraded vs. un-degraded parafoveal previews). Target words in sentences were presented in either black or blue and either underlined or normal. No effect of color and underlining, but a preview benefit could be detected for first pass reading measures. Fixation time measures that included re-reading, e.g., total viewing times, showed, in addition to a preview effect, a reduced fixation time for not highlighted (black not underlined) in contrast to highlighted target words (either blue or underlined or both). The present pattern reflects no detectable perceptual disadvantage of hyperlink stimuli but increased attraction of attention resources, after first pass reading, through highlighting. Blue or underlined text allows readers to easily perceive hypertext and at the same time readers re-visited highlighted words longer. On the basis of the present evidence, blue hypertext can be safely recommended to web designers for future use.

Literary and Electronic Hypertext: Borges, Criticism, Literary Research, and the Computer.

ERIC Educational Resources Information Center

Davison, Ned J.

1991-01-01

Examines what "hypertext" means to literary criticism on the one hand (i.e., intertextuality) and computing on the other, to determine how the two concepts may serve each other in a mutually productive way. (GLR)

A Hypertext Glossary of Nematology.

ERIC Educational Resources Information Center

Francl, Leonard J.

1993-01-01

Describes NEMATODE GLOSSARY, a hypertext glossary of terminology used in graduate nematology courses. Glossary definitions of anatomical terms are linked to color illustrations. Common names of plant and animal parasites and mnemonic codes for nematode genes are in separate appendices. (Author/MDH)

Interoperability In The New Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Rios, C.; Barbarisi, I.; Docasal, R.; Macfarlane, A. J.; Gonzalez, J.; Arviset, C.; Grotheer, E.; Besse, S.; Martinez, S.; Heather, D.; De Marchi, G.; Lim, T.; Fraga, D.; Barthelemy, M.

2015-12-01

As the world becomes increasingly interconnected, there is a greater need to provide interoperability with software and applications that are commonly being used globally. For this purpose, the development of the new Planetary Science Archive (PSA), by the European Space Astronomy Centre (ESAC) Science Data Centre (ESDC), is focused on building a modern science archive that takes into account internationally recognised standards in order to provide access to the archive through tools from third parties, for example by the NASA Planetary Data System (PDS), the VESPA project from the Virtual Observatory of Paris as well as other international institutions. The protocols and standards currently being supported by the new Planetary Science Archive at this time are the Planetary Data Access Protocol (PDAP), the EuroPlanet-Table Access Protocol (EPN-TAP) and Open Geospatial Consortium (OGC) standards. The architecture of the PSA consists of a Geoserver (an open-source map server), the goal of which is to support use cases such as the distribution of search results, sharing and processing data through a OGC Web Feature Service (WFS) and a Web Map Service (WMS). This server also allows the retrieval of requested information in several standard output formats like Keyhole Markup Language (KML), Geography Markup Language (GML), shapefile, JavaScript Object Notation (JSON) and Comma Separated Values (CSV), among others. The provision of these various output formats enables end-users to be able to transfer retrieved data into popular applications such as Google Mars and NASA World Wind.

Implications of the Java language on computer-based patient records.

PubMed

Pollard, D; Kucharz, E; Hammond, W E

1996-01-01

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

Variation in markup of general surgical procedures by hospital market concentration.

PubMed

Cerullo, Marcelo; Chen, Sophia Y; Dillhoff, Mary; Schmidt, Carl R; Canner, Joseph K; Pawlik, Timothy M

2018-04-01

Increasing hospital market concentration (with concomitantly decreasing hospital market competition) may be associated with rising hospital prices. Hospital markup - the relative increase in price over costs - has been associated with greater hospital market concentration. Patients undergoing a cardiothoracic or gastrointestinal procedure in the 2008-2011 Nationwide Inpatient Sample (NIS) were identified and linked to Hospital Market Structure Files. The association between market concentration, hospital markup and hospital for-profit status was assessed using mixed-effects log-linear models. A weighted total of 1,181,936 patients were identified. In highly concentrated markets, private for-profit status was associated with an 80.8% higher markup compared to public/private not-for-profit status (95%CI: +69.5% - +96.9%; p < 0.001). However, private for-profit status in highly concentrated markets was associated with only a 62.9% higher markup compared to public/private not-for-profit status in unconcentrated markets (95%CI: +45.4% - +81.1%; p < 0.001). Hospital for-profit status modified the association between hospitals' market concentration and markup. Government and private not-for-profit hospitals employed lower markups in more concentrated markets, whereas private for-profit hospitals employed higher markups in more concentrated markets. Copyright © 2017 Elsevier Inc. All rights reserved.

Applying Hypertext Structures to Software Documentation.

ERIC Educational Resources Information Center

French, James C.; And Others

1997-01-01

Describes a prototype system for software documentation management called SLEUTH (Software Literacy Enhancing Usefulness to Humans) being developed at the University of Virginia. Highlights include information retrieval techniques, hypertext links that are installed automatically, a WAIS (Wide Area Information Server) search engine, user…

Oak Regeneration: A Knowledge Synthesis

Treesearch

H. Michael Rauscher; David L. Loftis; Charles E. McGee; Christopher V. Worth

1997-01-01

This scientific literature is represented by a hypertext software. To view this literature you must download and install the hypertext software.Abstract: The scientific literature concerning oak regeneration problems is lengthy, complex, paradoxical, and often perplexing. Despite a large scientific literature and numerous conference...

Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information

PubMed Central

2016-01-01

Background Highlighted text in the Internet (i.e., hypertext) is predominantly blue and underlined. The perceptibility of these hypertext characteristics was heavily questioned by applied research and empirical tests resulted in inconclusive results. The ability to recognize blue text in foveal and parafoveal vision was identified as potentially constrained by the low number of foveally centered blue light sensitive retinal cells. The present study investigates if foveal and parafoveal perceptibility of blue hypertext is reduced in comparison to normal black text during reading. Methods A silent-sentence reading study with simultaneous eye movement recordings and the invisible boundary paradigm, which allows the investigation of foveal and parafoveal perceptibility, separately, was realized (comparing fixation times after degraded vs. un-degraded parafoveal previews). Target words in sentences were presented in either black or blue and either underlined or normal. Results No effect of color and underlining, but a preview benefit could be detected for first pass reading measures. Fixation time measures that included re-reading, e.g., total viewing times, showed, in addition to a preview effect, a reduced fixation time for not highlighted (black not underlined) in contrast to highlighted target words (either blue or underlined or both). Discussion The present pattern reflects no detectable perceptual disadvantage of hyperlink stimuli but increased attraction of attention resources, after first pass reading, through highlighting. Blue or underlined text allows readers to easily perceive hypertext and at the same time readers re-visited highlighted words longer. On the basis of the present evidence, blue hypertext can be safely recommended to web designers for future use. PMID:27688970

Comprehension and Navigation of Networked Hypertexts

ERIC Educational Resources Information Center

Blom, Helen; Segers, Eliane; Knoors, Harry; Hermans, Daan; Verhoeven, Ludo

2018-01-01

This study aims to investigate secondary school students' reading comprehension and navigation of networked hypertexts with and without a graphic overview compared to linear digital texts. Additionally, it was studied whether prior knowledge, vocabulary, verbal, and visual working memory moderated the relation between text design and…

Learning with Hypertext Learning Environments: Theory, Design, and Research.

ERIC Educational Resources Information Center

Jacobson, Michael J.; And Others

1996-01-01

Studied 69 undergraduates who used conceptually-indexed hypertext learning environments with differently structured thematic criss-crossing (TCC) treatments: guided and learner selected. Found that students need explicit modeling and scaffolding support to learn complex knowledge from these learning environments, and considers implications for…

Hypertext, Hypermedia, and Metacognition: Research and Instructional Implications for Disabled Readers.

ERIC Educational Resources Information Center

Balajthy, Ernest

1990-01-01

The article examines the potential impact of computer-based text technologies, called hypermedia, on disabled readers. Discussed are hypertext, the hypercard, and implications of metacognitive research (such as author versus user control over text manipulations), instructional implications, and instructional text engineering. (DB)

A Bibliography on Hypertext and Hypermedia with Selected Annotations.

ERIC Educational Resources Information Center

Franklin, Carl

1990-01-01

The first of 2 parts, this bibliography contains 233 references to materials dealing with hypertext and hypermedia. Entries are presented in the following categories: alternatives to HyperCard; bibliographies; biographies; books and book reviews; dictionaries; hardware; interviews; library applications; optical disk-related; theoretical and…

Baseline coastal oblique aerial photographs collected from Owls Head, Maine, to the Virginia/North Carolina border, May 19-22, 2009

USGS Publications Warehouse

Morgan, Karen L.M.; Hapke, Cheryl J.; Himmelstoss, Emily A.

2015-01-01

Table 1 provides detailed information about the GPS location, name, date, and time for each of the 12,726 photographs taken along with links to each photograph. In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files

Amelie: A Recombinant Computing Framework for Ambient Awareness

NASA Astrophysics Data System (ADS)

Metaxas, Georgios; Markopoulos, Panos; Aarts, Emile

This paper presents Amelie, a service oriented framework that supports the implementation of awareness systems. Amelie adopts the tenets of Recombinant computing to address an important non-functional requirement for Ambient Intelligence software, namely the heterogeneous combination of services and components. Amelie is founded upon FN-AAR an abstract model of Awareness Systems which enables the immediate expression and implementation of socially salient requirements, such as symmetry and social translucence. We discuss the framework and show how system behaviours can be specified using the Awareness Mark-up Language AML.

The semantic architecture of the World-Wide Molecular Matrix (WWMM)

PubMed Central

2011-01-01

The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption. PMID:21999475

The semantic architecture of the World-Wide Molecular Matrix (WWMM).

PubMed

Murray-Rust, Peter; Adams, Sam E; Downing, Jim; Townsend, Joe A; Zhang, Yong

2011-10-14

The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.

The semantics of Chemical Markup Language (CML): dictionaries and conventions.

PubMed

Murray-Rust, Peter; Townsend, Joe A; Adams, Sam E; Phadungsukanan, Weerapong; Thomas, Jens

2011-10-14

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.

Records and history of the United States Geological Survey

USGS Publications Warehouse

Nelson, Clifford M.

2000-01-01

This publication contains two presentations in Portable Document Format (PDF). The first is Renee M. Jaussaud's inventory of the documents accessioned by the end of 1997 into Record Group 57 (Geological Survey) at the National Archives and Records Administration's (NARA) Archives II facility in College Park, Md., but not the materials in NARA's regional archives. The second is Mary C. Rabbitt's 'The United States Geological Survey 1879-1989,' which appeared in 1989 as USGS Circular 1050. Additionally, USGS Circular 1050 is also presented in Hyper Text Markup Language (HTML) format.

CMLLite: a design philosophy for CML

PubMed Central

2011-01-01

CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service. PMID:21999395

The semantics of Chemical Markup Language (CML): dictionaries and conventions

PubMed Central

2011-01-01

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs. PMID:21999509

Rehabilitation R@D Progress Reports, 1992-1993. Volume 30-31

DTIC Science & Technology

1993-01-01

Transcripts of the videotape are being ana- lyzed on a hypertext database and also by qualitative data analysis software ( NUDIST ) to determine elements...number of videotapes have been transcribed and are being analyzed by the hypertext and NUDIST software. The first cycle is in progress, reflecting

The Liberating Teaching Methods of the Brazilian Paulo Freire and Hypertext.

ERIC Educational Resources Information Center

Gomez-Martinez, Jose Luis

2003-01-01

Exemplifies, through the pedagogical theories put forth by Paulo Freire in his book "Pedagogia del oprimado" (teaching the oppressed) and along with the potentials of hypertext, the intimate relationship between socio-cultural forces and the technical responses emerging from the dialectic process between them. (AS)

Down the Yellow Chip Road: Hypertext Portfolios in Oz.

ERIC Educational Resources Information Center

Fischer, Katherine M.

1996-01-01

Describes a creative writing class in which students used hypertext to develop their writing portfolios. Suggests that, much like "Kansas Dorothy" who ventured into Oz, a "tornado" carried these students and their teacher from the safe Paperland to the yellow chip road of electronic portfolios. Notes that students' portfolios…

Elaborated Resources: An Instructional Design Strategy for Hypermedia.

ERIC Educational Resources Information Center

Rezabek, Randall H.; Ragan, Tillman J.

The concept of hypertext was introduced by Ted Nelson in 1965, but only recently has the widely available technology caught up with the idea. The new generation of microcomputers featuring large internal memories, graphic interfaces, and large data storage capacities have made the commercial development of hypertext/hypermedia software possible. A…

Effects of External Learning Aids on Learning with Ill-Structured Hypertext.

ERIC Educational Resources Information Center

Astleitner, Hermann

1997-01-01

Describes three experiments with high school and college students concerning learning with ill-structured hypertext; in each study, one different kind of external learning aid (memo pads, learning time, and teaching objectives) was manipulated and examined for its effect on intentional and incidental knowledge acquisition. Findings are discussed…

Seamless Merging of Hypertext and Algorithm Animation

ERIC Educational Resources Information Center

Karavirta, Ville

2009-01-01

Online learning material that students use by themselves is one of the typical usages of algorithm animation (AA). Thus, the integration of algorithm animations into hypertext is seen as an important topic today to promote the usage of algorithm animation in teaching. This article presents an algorithm animation viewer implemented purely using…

Landmarks in the World Wide Web: A Preliminary Study.

ERIC Educational Resources Information Center

Heffron, Jennifer K.; Dillon, Andrew; Mostafa, Javed

1996-01-01

Outlines results of a pilot study examining what constitutes a landmark in hypertext. Seven subjects began a search task from the same Indiana University School of Library and Information Science Homepage; searches had to be conducted without the use of search engines, and strictly following hypertext links. (Author/AEF)

WorldWide Web: Hypertext from CERN.

ERIC Educational Resources Information Center

Nickerson, Gord

1992-01-01

Discussion of software tools for accessing information on the Internet focuses on the WorldWideWeb (WWW) system, which was developed at the European Particle Physics Laboratory (CERN) in Switzerland to build a worldwide network of hypertext links using available networking technology. Its potential for use with multimedia documents is also…

48 CFR 552.243-71 - Equitable Adjustments.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Markups. (3) Change to the time for completion specified in the contract. (e) Direct costs. The Contractor... contract regarding the Contractor's project schedule. (h) Markups. For each firm whose direct costs are... applicable, a bond rate and insurance rate. Markups shall be determined and applied as follows: (1) Overhead...

Competition in the economic crisis: Analysis of procurement auctions.

PubMed

Gugler, Klaus; Weichselbaumer, Michael; Zulehner, Christine

2015-01-01

We study the effects of the recent economic crisis on firms׳ bidding behavior and markups in sealed bid auctions. Using data from Austrian construction procurements, we estimate bidders׳ construction costs within a private value auction model. We find that markups of all bids submitted decrease by 1.5 percentage points in the recent economic crisis, markups of winning bids decrease by 3.3 percentage points. We also find that without the government stimulus package this decrease would have been larger. These two pieces of evidence point to pro-cyclical markups.

The caBIG annotation and image Markup project.

PubMed

Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

2010-04-01

Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

PubMed Central

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-01-01

Background Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. Results We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. Conclusion By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions. PMID:18570683

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.

Systematic reconstruction of TRANSPATH data into cell system markup language.

PubMed

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-06-23

Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.

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.

Rethinking Joseph Janangelo's "Joseph Cornell and the Artistry of Composing Persuasive Hypertexts"

ERIC Educational Resources Information Center

College Composition and Communication, 2007

2007-01-01

This article presents several excerpts from an article written by Joseph Janangelo titled "Joseph Cornell and the Artistry of Composing Persuasive Hypertexts." In his article, Janangelo suggested that Cornell's work and ideas about composing model intelligent ways to composing persuasive nonsequential text. Janangelo also wondered if the use of…

E-Learning Today: A Review of Research on Hypertext Comprehension

ERIC Educational Resources Information Center

Hinesley, Gail A.

2007-01-01

Use of hypertext is pervasive in education today--it is used for all online course delivery as well as many stand-alone delivery methods such as educational computer software and compact discs (CDs). This article will review Kintsch's Construction-Integration and Anderson's Adaptive Control of Thought-Rational (ACT-R) cognitive architectures and…

Extended Subject Access to Hypertext Online Documentation. Part III: The Document-Boundaries Problem.

ERIC Educational Resources Information Center

Girill, T. R.

1991-01-01

This article continues the description of DFT (Document, Find, Theseus), an online documentation system that provides computer-managed on-demand printing of software manuals as well as the interactive retrieval of reference passages. Document boundaries in the hypertext database are discussed, search vocabulary complexities are described, and text…

Working Memory Capacity and Reading Skill Moderate the Effectiveness of Strategy Training in Learning from Hypertext

ERIC Educational Resources Information Center

Naumann, Johannes; Richter, Tobias; Christmann, Ursula; Groeben, Norbert

2008-01-01

Cognitive and metacognitive strategies are particularly important for learning with hypertext. The effectiveness of strategy training, however, depends on available working memory resources. Thus, especially learners high on working memory capacity can profit from strategy training, while learners low on working memory capacity might easily be…

Working Memory Capacity and L2 University Students' Comprehension of Linear Texts and Hypertexts

ERIC Educational Resources Information Center

Fontanini, Ingrid; Tomitch, Leda Maria Braga

2009-01-01

The aim of this study was to investigate the relationship between working memory capacity and L2 reading comprehension of both linear texts and hypertexts. Three different instruments were used to measure comprehension (recall, comprehension questions and perception of contradictions) and the Reading Span Test (Daneman & Carpenter, 1980) was…

Navigation Maps in a Computer-Networked Hypertext Learning System.

ERIC Educational Resources Information Center

Chou, Chien; Lin, Hua

A study of first-year college students (n=121) in Taiwan investigated the effects of navigation maps and learner cognitive styles on performance in searches for information, estimation of course scope, and the development of cognitive maps within a hypertext learning course. Students were tested to determine level of perceptual field dependence…

Recent Literature Shows Accelerated Growth in Hypermedia Tools: An Annotated Bibliography.

ERIC Educational Resources Information Center

Gabbard, Ralph

1994-01-01

Presents an annotated bibliography of materials on hypertext/hypermedia. Information available on the World Wide Web is described; journals that cover hypermedia are listed; and the main bibliography is divided into 3 sections on general hypertext applications (17 titles), DOS/Windows applications (17 titles), and HyperCard applications (18…

Multiple Views, Contexts, and Symbol Systems in Learning with Hypertext/Hypermedia: A Critical Review of Research.

ERIC Educational Resources Information Center

Tergan, Sigmar-Olaf

1997-01-01

Reviews research on the effectiveness of hypertext/hypermedia-based learning and concludes that presenting subject matter from different perspectives, in multiple contexts, and in multiple codes does not automatically contribute to higher performance but may when instructional scaffolding is provided. The additional cognitive load may actually…

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

PubMed

Frank, M S; Dreyer, K

2001-06-01

We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.

PubMed

Mueller, Martina; Wagner, Carol L; Annibale, David J; Knapp, Rebecca G; Hulsey, Thomas C; Almeida, Jonas S

2006-03-01

Approximately 30% of intubated preterm infants with respiratory distress syndrome (RDS) will fail attempted extubation, requiring reintubation and mechanical ventilation. Although ventilator technology and monitoring of premature infants have improved over time, optimal extubation remains challenging. Furthermore, extubation decisions for premature infants require complex informational processing, techniques implicitly learned through clinical practice. Computer-aided decision-support tools would benefit inexperienced clinicians, especially during peak neonatal intensive care unit (NICU) census. A five-step procedure was developed to identify predictive variables. Clinical expert (CE) thought processes comprised one model. Variables from that model were used to develop two mathematical models for the decision-support tool: an artificial neural network (ANN) and a multivariate logistic regression model (MLR). The ranking of the variables in the three models was compared using the Wilcoxon Signed Rank Test. The best performing model was used in a web-based decision-support tool with a user interface implemented in Hypertext Markup Language (HTML) and the mathematical model employing the ANN. CEs identified 51 potentially predictive variables for extubation decisions for an infant on mechanical ventilation. Comparisons of the three models showed a significant difference between the ANN and the CE (p = 0.0006). Of the original 51 potentially predictive variables, the 13 most predictive variables were used to develop an ANN as a web-based decision-tool. The ANN processes user-provided data and returns the prediction 0-1 score and a novelty index. The user then selects the most appropriate threshold for categorizing the prediction as a success or failure. Furthermore, the novelty index, indicating the similarity of the test case to the training case, allows the user to assess the confidence level of the prediction with regard to how much the new data differ from the data originally used for the development of the prediction tool. State-of-the-art, machine-learning methods can be employed for the development of sophisticated tools to aid clinicians' decisions. We identified numerous variables considered relevant for extubation decisions for mechanically ventilated premature infants with RDS. We then developed a web-based decision-support tool for clinicians which can be made widely available and potentially improve patient care world wide.

Web-based X-ray quality control documentation.

PubMed

David, George; Burnett, Lou Ann; Schenkel, Robert

2003-01-01

The department of radiology at the Medical College of Georgia Hospital and Clinics has developed an equipment quality control web site. Our goal is to provide immediate access to virtually all medical physics survey data. The web site is designed to assist equipment engineers, department management and technologists. By improving communications and access to equipment documentation, we believe productivity is enhanced. The creation of the quality control web site was accomplished in three distinct steps. First, survey data had to be placed in a computer format. The second step was to convert these various computer files to a format supported by commercial web browsers. Third, a comprehensive home page had to be designed to provide convenient access to the multitude of surveys done in the various x-ray rooms. Because we had spent years previously fine-tuning the computerization of the medical physics quality control program, most survey documentation was already in spreadsheet or database format. A major technical decision was the method of conversion of survey spreadsheet and database files into documentation appropriate for the web. After an unsatisfactory experience with a HyperText Markup Language (HTML) converter (packaged with spreadsheet and database software), we tried creating Portable Document Format (PDF) files using Adobe Acrobat software. This process preserves the original formatting of the document and takes no longer than conventional printing; therefore, it has been very successful. Although the PDF file generated by Adobe Acrobat is a proprietary format, it can be displayed through a conventional web browser using the freely distributed Adobe Acrobat Reader program that is available for virtually all platforms. Once a user installs the software, it is automatically invoked by the web browser whenever the user follows a link to a file with a PDF extension. Although no confidential patient information is available on the web site, our legal department recommended that we secure the site in order to keep out those wishing to make mischief. Our interim solution has not been to password protect the page, which we feared would hinder access for occasional legitimate users, but also not to provide links to it from other hospital and department pages. Utility and productivity were improved and time and money were saved by making radiological equipment quality control documentation instantly available on-line.

Using XML and Java Technologies for Astronomical Instrument Control

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

Application of XML to Journal Table Archiving

NASA Astrophysics Data System (ADS)

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

1998-12-01

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

A program code generator for multiphysics biological simulation using markup languages.

PubMed

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

[Research on tumor information grid framework].

PubMed

Zhang, Haowei; Qin, Zhu; Liu, Ying; Tan, Jianghao; Cao, Haitao; Chen, Youping; Zhang, Ke; Ding, Yuqing

2013-10-01

In order to realize tumor disease information sharing and unified management, we utilized grid technology to make the data and software resources which distributed in various medical institutions for effective integration so that we could make the heterogeneous resources consistent and interoperable in both semantics and syntax aspects. This article describes the tumor grid framework, the type of the service being packaged in Web Service Description Language (WSDL) and extensible markup language schemas definition (XSD), the client use the serialized document to operate the distributed resources. The service objects could be built by Unified Modeling Language (UML) as middle ware to create application programming interface. All of the grid resources are registered in the index and released in the form of Web Services based on Web Services Resource Framework (WSRF). Using the system we can build a multi-center, large sample and networking tumor disease resource sharing framework to improve the level of development in medical scientific research institutions and the patient's quality of life.

Data on the interexaminer variation of minutia markup on latent fingerprints.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2016-09-01

The data in this article supports the research paper entitled "Interexaminer variation of minutia markup on latent fingerprints" [1]. The data in this article describes the variability in minutia markup during both analysis of the latents and comparison between latents and exemplars. The data was collected in the "White Box Latent Print Examiner Study," in which each of 170 volunteer latent print examiners provided detailed markup documenting their examinations of latent-exemplar pairs of prints randomly assigned from a pool of 320 pairs. Each examiner examined 22 latent-exemplar pairs; an average of 12 examiners marked each latent.

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

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

NASA Technical Reports Server (NTRS)

Nash, Brent; DeMore, Martha

2009-01-01

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

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Limitation on use of HTML... Requirements § 232.105 Limitation on use of HTML documents and hypertext links. (a) Electronic filers must... EDGAR database on the Commission's public web site (www.sec.gov). Electronic filers also may include...

Hyperlink Format, Categorization Abilities and Memory Span as Contributors to Deaf Users Hypertext Access

ERIC Educational Resources Information Center

Farjardo, Inmaculada; Arfe, Barbara; Benedetti, Patrizia; Altoe, Gianmarco

2008-01-01

Sixty deaf and hearing students were asked to search for goods in a Hypertext Supermarket with either graphical or textual links of high typicality, frequency, and familiarity. Additionally, they performed a picture and word categorization task and two working memory span tasks (spatial and verbal). Results showed that deaf students were faster in…

Reconceptualising Pedagogy: Students' Hypertext Stories with Pictures and Words.

ERIC Educational Resources Information Center

Russell, Glenn

Hypertext software permits students to write non-linear stories which include pictures and words. The characteristics of these stories may be affected by student and teacher understandings of how pictures and words may be combined to produce meanings for the reader. The use of images and words in comic books and children's picture-books contribute…

The Effect of Hypertext Annotation Presentation Formats on Perceived Cognitive Load and Learner Control

ERIC Educational Resources Information Center

Yao, Yuanming; Gill, Michele

2009-01-01

The impact of hypertext presentation formats on learner control and cognitive load was examined in this study using Campbell and Stanley's (1963) Posttest Only Control Group design. One hundred eighty-six undergraduate students were randomly assigned to read a web-based text with no annotations, online glossary annotations, embedded annotations,…

The Influence of Self-Regulated Learning and Prior Knowledge on Knowledge Acquisition in Computer-Based Learning Environments

ERIC Educational Resources Information Center

Bernacki, Matthew

2010-01-01

This study examined how learners construct textbase and situation model knowledge in hypertext computer-based learning environments (CBLEs) and documented the influence of specific self-regulated learning (SRL) tactics, prior knowledge, and characteristics of the learner on posttest knowledge scores from exposure to a hypertext. A sample of 160…

User Evaluation of Automatically Generated Semantic Hypertext Links in a Heavily Used Procedural Manual.

ERIC Educational Resources Information Center

Tebbutt, John

1999-01-01

Discusses efforts at National Institute of Standards and Technology (NIST) to construct an information discovery tool through the fusion of hypertext and information retrieval that works by parsing a contiguous document base into smaller documents and inserting semantic links between them. Also presents a case study that evaluated user reactions.…

Hypertext-based design of a user interface for scheduling

NASA Technical Reports Server (NTRS)

Woerner, Irene W.; Biefeld, Eric

1993-01-01

Operations Mission Planner (OMP) is an ongoing research project at JPL that utilizes AI techniques to create an intelligent, automated planning and scheduling system. The information space reflects the complexity and diversity of tasks necessary in most real-world scheduling problems. Thus the problem of the user interface is to present as much information as possible at a given moment and allow the user to quickly navigate through the various types of displays. This paper describes a design which applies the hypertext model to solve these user interface problems. The general paradigm is to provide maps and search queries to allow the user to quickly find an interesting conflict or problem, and then allow the user to navigate through the displays in a hypertext fashion.

Semantic Markup for Literary Scholars: How Descriptive Markup Affects the Study and Teaching of Literature.

ERIC Educational Resources Information Center

Campbell, D. Grant

2002-01-01

Describes a qualitative study which investigated the attitudes of literary scholars towards the features of semantic markup for primary texts in XML format. Suggests that layout is a vital part of the reading process which implies that the standardization of DTDs (Document Type Definitions) should extend to styling as well. (Author/LRW)

Design and implementation of an internet-based electrical engineering laboratory.

PubMed

He, Zhenlei; Shen, Zhangbiao; Zhu, Shanan

2014-09-01

This paper describes an internet-based electrical engineering laboratory (IEE-Lab) with virtual and physical experiments at Zhejiang University. In order to synthesize the advantages of both experiment styles, the IEE-Lab is come up with Client/Server/Application framework and combines the virtual and physical experiments. The design and workflow of IEE-Lab are introduced. The analog electronic experiment is taken as an example to show Flex plug-in design, data communication based on XML (Extensible Markup Language), experiment simulation modeled by Modelica and control terminals' design. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

MXA: a customizable HDF5-based data format for multi-dimensional data sets

NASA Astrophysics Data System (ADS)

Jackson, M.; Simmons, J. P.; De Graef, M.

2010-09-01

A new digital file format is proposed for the long-term archival storage of experimental data sets generated by serial sectioning instruments. The format is known as the multi-dimensional eXtensible Archive (MXA) format and is based on the public domain Hierarchical Data Format (HDF5). The MXA data model, its description by means of an eXtensible Markup Language (XML) file with associated Document Type Definition (DTD) are described in detail. The public domain MXA package is available through a dedicated web site (mxa.web.cmu.edu), along with implementation details and example data files.

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

NASA Technical Reports Server (NTRS)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

77 FR 47896 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-10

... that it is appropriate to charge a markup with respect to directed orders to reflect the costs of offering routing services and the value of such services. Notably, in all instances NASDAQ charges a markup... that it does not currently charge a markup with respect to non-directed orders that are routed to PSX...

Application of whole slide image markup and annotation for pathologist knowledge capture.

PubMed

Campbell, Walter S; Foster, Kirk W; Hinrichs, Steven H

2013-01-01

The ability to transfer image markup and annotation data from one scanned image of a slide to a newly acquired image of the same slide within a single vendor platform was investigated. The goal was to study the ability to use image markup and annotation data files as a mechanism to capture and retain pathologist knowledge without retaining the entire whole slide image (WSI) file. Accepted mathematical principles were investigated as a method to overcome variations in scans of the same glass slide and to accurately associate image markup and annotation data across different WSI of the same glass slide. Trilateration was used to link fixed points within the image and slide to the placement of markups and annotations of the image in a metadata file. Variation in markup and annotation placement between WSI of the same glass slide was reduced from over 80 μ to less than 4 μ in the x-axis and from 17 μ to 6 μ in the y-axis (P < 0.025). This methodology allows for the creation of a highly reproducible image library of histopathology images and interpretations for educational and research use.

Application of whole slide image markup and annotation for pathologist knowledge capture

PubMed Central

Campbell, Walter S.; Foster, Kirk W.; Hinrichs, Steven H.

2013-01-01

Objective: The ability to transfer image markup and annotation data from one scanned image of a slide to a newly acquired image of the same slide within a single vendor platform was investigated. The goal was to study the ability to use image markup and annotation data files as a mechanism to capture and retain pathologist knowledge without retaining the entire whole slide image (WSI) file. Methods: Accepted mathematical principles were investigated as a method to overcome variations in scans of the same glass slide and to accurately associate image markup and annotation data across different WSI of the same glass slide. Trilateration was used to link fixed points within the image and slide to the placement of markups and annotations of the image in a metadata file. Results: Variation in markup and annotation placement between WSI of the same glass slide was reduced from over 80 μ to less than 4 μ in the x-axis and from 17 μ to 6 μ in the y-axis (P < 0.025). Conclusion: This methodology allows for the creation of a highly reproducible image library of histopathology images and interpretations for educational and research use. PMID:23599902

How do students navigate and learn from nonlinear science texts: Can metanavigation support promote science learning?

NASA Astrophysics Data System (ADS)

Stylianou, Agni

2003-06-01

Digital texts which are based on hypertext and hypermedia technologies are now being used to support science learning. Hypertext offers certain opportunities for learning as well as difficulties that challenge readers to become metacognitively aware of their navigation decisions in order to trade both meaning and structure while reading. The goal of this study was to investigate whether supporting sixth grade students to monitor and regulate their navigation behavior while reading from hypertext would lead to better navigation and learning. Metanavigation support in the form of prompts was provided to groups of students who used a hypertext system called CoMPASS to complete a design challenge. The metanavigation prompts aimed at encouraging students to understand the affordances of the navigational aids in CoMPASS and use them to guide their navigation. The study was conducted in a real classroom setting during the implementation of CoMPASS in sixth grade science classes. Multiple sources of group and individual data were collected and analyzed. Measures included student's individual performance in a pre-science knowledge test, the Metacognitive Awareness of Reading Strategies Inventory (MARSI), a reading comprehension test and a concept map test. Process measures included log file information that captured group navigation paths during the use of CoMPASS. The results suggested that providing metanavigation support enabled the groups to make coherent transitions among the text units. Findings also revealed that reading comprehension, presence of metanavigation support and prior domain knowledge significantly predicted students' individual understanding of science. Implications for hypertext design and literacy research fields are discussed.

Improving the Conceptual Understanding in Kinematics Subject Matter with Hypertext Media Learning and Formal Thinking

ERIC Educational Resources Information Center

Manurung, Sondang R.; Mihardi, Satria

2016-01-01

The purpose of this study was to determine the effectiveness of hypertext media based kinematic learning and formal thinking ability to improve the conceptual understanding of physic prospective students. The research design used is the one-group pretest-posttest experimental design is carried out in the research by taking 36 students on from…

On the Creation of Hypertext Links in Full-Text Documents: Measurement of Inter-Linker Consistency.

ERIC Educational Resources Information Center

Ellis, David; And Others

1994-01-01

Describes a study in which several different sets of hypertext links are inserted by different people in full-text documents. The degree of similarity between the sets is measured using coefficients and topological indices. As in comparable studies of inter-indexer consistency, the sets of links used by different people showed little similarity.…

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2014 CFR

2014-04-01

... submit the following documents in ASCII: Form N-SAR (§ 274.101 of this chapter) and Form 13F (§ 249.325... exhibits to Form N-SAR in HTML. (b) Electronic filers may not include in any HTML document hypertext links... documents within the current submission and to documents previously filed electronically and located in the...

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2013 CFR

2013-04-01

... submit the following documents in ASCII: Form N-SAR (§ 274.101 of this chapter) and Form 13F (§ 249.325... exhibits to Form N-SAR in HTML. (b) Electronic filers may not include in any HTML document hypertext links... documents within the current submission and to documents previously filed electronically and located in the...

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2011 CFR

2011-04-01

... submit the following documents in ASCII: Form N-SAR (§ 274.101 of this chapter) and Form 13F (§ 249.325... exhibits to Form N-SAR in HTML. (b) Electronic filers may not include in any HTML document hypertext links... documents within the current submission and to documents previously filed electronically and located in the...

17 CFR 232.105 - Limitation on use of HTML documents and hypertext links.

Code of Federal Regulations, 2012 CFR

2012-04-01

... submit the following documents in ASCII: Form N-SAR (§ 274.101 of this chapter) and Form 13F (§ 249.325... exhibits to Form N-SAR in HTML. (b) Electronic filers may not include in any HTML document hypertext links... documents within the current submission and to documents previously filed electronically and located in the...

Computer integrated documentation

NASA Technical Reports Server (NTRS)

Boy, Guy

1991-01-01

The main technical issues of the Computer Integrated Documentation (CID) project are presented. The problem of automation of documents management and maintenance is analyzed both from an artificial intelligence viewpoint and from a human factors viewpoint. Possible technologies for CID are reviewed: conventional approaches to indexing and information retrieval; hypertext; and knowledge based systems. A particular effort was made to provide an appropriate representation for contextual knowledge. This representation is used to generate context on hypertext links. Thus, indexing in CID is context sensitive. The implementation of the current version of CID is described. It includes a hypertext data base, a knowledge based management and maintenance system, and a user interface. A series is also presented of theoretical considerations as navigation in hyperspace, acquisition of indexing knowledge, generation and maintenance of a large documentation, and relation to other work.

Distributed framework for dyanmic telescope and instrument control

NASA Astrophysics Data System (ADS)

Ames, Troy J.; Case, Lynne

2003-02-01

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

Design and study of geosciences data share platform :platform framework, data interoperability, share approach

NASA Astrophysics Data System (ADS)

Lu, H.; Yi, D.

2010-12-01

The Deep Exploration is one of the important approaches to the Geoscience research. Since 1980s we had started it and achieved a lot of data. Researchers usually integrate both data of space exploration and deep exploration to study geological structures and represent the Earth’s subsurface, and analyze and explain on the base of integrated data. Due to the different exploration approach it results the heterogeneity of data, and therefore the data achievement is always of the import issue to make the researchers confused. The problem of data share and interaction has to be solved during the development of the SinoProbe research project. Through the research of domestic and overseas well-known exploration project and geosciences data platform, the subject explores the solution of data share and interaction. Based on SOA we present the deep exploration data share framework which comprises three level: data level is used for the solution of data store and the integration of the heterogeneous data; medial level provides the data service of geophysics, geochemistry, etc. by the means of Web service, and carry out kinds of application combination by the use of GIS middleware and Eclipse RCP; interaction level provides professional and non-professional customer the access to different accuracy data. The framework adopts GeoSciML data interaction approach. GeoSciML is a geosciences information markup language, as an application of the OpenGIS Consortium’s (OGC) Geography Markup Language (GML). It transfers heterogeneous data into one earth frame and implements inter-operation. We dissertate in this article the solution how to integrate the heterogeneous data and share the data in the project of SinoProbe.

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.

Hypertext and Multimedia for Functional Enhancement of USARIEM Medical Handbooks and Biomedical Simulation Software.

DTIC Science & Technology

1994-12-01

complex Internet addresses. Hypertext and hypermedia documents have logical and physical structure (Shneiderman, 1993). The logical structure delineates...Rubra, Miliaria Profunda , Anhidrotic Heat Exhaustion, Heat Syncope, Heat Edema, Sunburn, and Heat Tetany. The user may return to the main document...military or scientific organizations via digital communications networks such as the Internet . Access clearance would first be obtained from the USARIEM

The need for the use of XACML access control policy in a distributed EHR and some performance considerations.

PubMed

Sucurovic, Snezana; Milutinovic, Veljko

2008-01-01

The Internet based distributed large scale information systems implements attribute based access control (ABAC) rather than Role Based Access Control (RBAC). The reason is that the Internet is identity less and that ABAC scales better. EXtensible Access Control Markup Language is standardized language for writing access control policies, access control requests and access control responses in ABAC. XACML can provide decentralized administration and credentials distribution. In year 2002 version of CEN ENV 13 606 attributes have been attached to EHCR components and in such a system ABAC and XACML have been easy to implement. This paper presents writing XACML policies in the case when attributes are in hierarchical structure. It is presented two possible solutions to write XACML policy in that case and that the solution when set functions are used is more compact and provides 10% better performances.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

A Journey in Standard Development: The Core Manufacturing Simulation Data (CMSD) Information Model.

PubMed

Lee, Yung-Tsun Tina

2015-01-01

This report documents a journey "from research to an approved standard" of a NIST-led standard development activity. That standard, Core Manufacturing Simulation Data (CMSD) information model, provides neutral structures for the efficient exchange of manufacturing data in a simulation environment. The model was standardized under the auspices of the international Simulation Interoperability Standards Organization (SISO). NIST started the research in 2001 and initiated the standardization effort in 2004. The CMSD standard was published in two SISO Products. In the first Product, the information model was defined in the Unified Modeling Language (UML) and published in 2010 as SISO-STD-008-2010. In the second Product, the information model was defined in Extensible Markup Language (XML) and published in 2013 as SISO-STD-008-01-2012. Both SISO-STD-008-2010 and SISO-STD-008-01-2012 are intended to be used together.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

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

Interexaminer variation of minutia markup on latent fingerprints.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2016-07-01

Latent print examiners often differ in the number of minutiae they mark during analysis of a latent, and also during comparison of a latent with an exemplar. Differences in minutia counts understate interexaminer variability: examiners' markups may have similar minutia counts but differ greatly in which specific minutiae were marked. We assessed variability in minutia markup among 170 volunteer latent print examiners. Each provided detailed markup documenting their examinations of 22 latent-exemplar pairs of prints randomly assigned from a pool of 320 pairs. An average of 12 examiners marked each latent. The primary factors associated with minutia reproducibility were clarity, which regions of the prints examiners chose to mark, and agreement on value or comparison determinations. In clear areas (where the examiner was "certain of the location, presence, and absence of all minutiae"), median reproducibility was 82%; in unclear areas, median reproducibility was 46%. Differing interpretations regarding which regions should be marked (e.g., when there is ambiguity in the continuity of a print) contributed to variability in minutia markup: especially in unclear areas, marked minutiae were often far from the nearest minutia marked by a majority of examiners. Low reproducibility was also associated with differences in value or comparison determinations. Lack of standardization in minutia markup and unfamiliarity with test procedures presumably contribute to the variability we observed. We have identified factors accounting for interexaminer variability; implementing standards for detailed markup as part of documentation and focusing future training efforts on these factors may help to facilitate transparency and reduce subjectivity in the examination process. Published by Elsevier Ireland Ltd.

[Use of hypertext as information and training tools in the prevention of occupational risk].

PubMed

Franco, G

1998-01-01

Modern medical education is based on a variety of teaching techniques, by means of which individuals learn most effectively. The availability of the new technologies together with the diffusion of personal computers is favouring the spreading of the use of hypertexts through the World Wide Web. This contribution describes 2 hypertexts ("Human Activities and Health Risk"; "Occupation, Risk and Disease. A Problem-Oriented Hypertext-Tool to Learn Occupational Medicine") and the prototype "Virtual Hospital". Assuming that prevention of health risks is based upon their knowledge, they have been created with the aim of providing users with problem-oriented tools, whose retorical aspects (content, information organization, user interface) are analysed. The "Human Activities and Health Risk" deals with the description of working activities and allows user to recognize health risks. The "Occupation, Risk and Disease. A Problem-Oriented Hypertext-Tool to Learn Occupational Medicine" embodies a case report containing the clustered information about the patient and the library including educational material (risk factors, symptoms and signs, organ system diseases, jobs, occupational risk factors, environment related diseases. The "Virtual Hospital" has been conceived assuming that an appropriate information can change workers' behaviour in hospital, where health risks can be often underevaluated. It consists of a variety of structured and unstructured information, which can be browsed by users, allowing the discovery of links and providing the awareness of the semantic relationship between related information elements (including environment, instruments, drugs, job analysis, situations at risk for health, preventive means). The "Virtual Hospital" aims making the understanding of the working situations at risk easier and more interesting, stimulating the awareness of the relationship between jobs and risks.

Facilitating access to information in large documents with an intelligent hypertext system

NASA Technical Reports Server (NTRS)

Mathe, Nathalie

1993-01-01

Retrieving specific information from large amounts of documentation is not an easy task. It could be facilitated if information relevant in the current problem solving context could be automatically supplied to the user. As a first step towards this goal, we have developed an intelligent hypertext system called CID (Computer Integrated Documentation) and tested it on the Space Station Freedom requirement documents. The CID system enables integration of various technical documents in a hypertext framework and includes an intelligent context-sensitive indexing and retrieval mechanism. This mechanism utilizes on-line user information requirements and relevance feedback either to reinforce current indexing in case of success or to generate new knowledge in case of failure. This allows the CID system to provide helpful responses, based on previous usage of the documentation, and to improve its performance over time.

The inclusion of an online journal in PubMed central - a difficult path.

PubMed

Grech, Victor

2016-01-01

The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database.

Post-Hurricane Ivan coastal oblique aerial photographs collected from Crawfordville, Florida, to Petit Bois Island, Mississippi, September 17, 2004

USGS Publications Warehouse

Morgan, Karen L.M.; Krohn, M. Dennis; Peterson, Russell D.; Thompson, Philip R.; Subino, Janice A.

2015-01-01

Table 1 provides detailed information about the GPS location, image name, date, and time for each of the 3,381 photographs taken, along with links to each photograph. The photographs are organized into segments, also referred to as contact sheets, and represent approximately 5 minutes of flight time. In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided, which can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

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

PubMed

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

2011-01-01

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

Variation in Emergency Department vs Internal Medicine Excess Charges in the United States.

PubMed

Xu, Tim; Park, Angela; Bai, Ge; Joo, Sarah; Hutfless, Susan M; Mehta, Ambar; Anderson, Gerard F; Makary, Martin A

2017-08-01

Uninsured and insured but out-of-network emergency department (ED) patients are often billed hospital chargemaster prices, which exceed amounts typically paid by insurers. To examine the variation in excess charges for services provided by emergency medicine and internal medicine physicians. Retrospective analysis was conducted of professional fee payment claims made by the Centers for Medicare & Medicaid Services for all services provided to Medicare Part B fee-for-service beneficiaries in calendar year 2013. Data analysis was conducted from January 1 to July 31, 2016. Markup ratios for ED and internal medicine professional services, defined as the charges submitted by the hospital divided by the Medicare allowable amount. Our analysis included 12 337 emergency medicine physicians from 2707 hospitals and 57 607 internal medicine physicians from 3669 hospitals in all 50 states. Services provided by emergency medicine physicians had an overall markup ratio of 4.4 (340% excess charges), which was greater than the markup ratio of 2.1 (110% excess charges) for all services performed by internal medicine physicians. Markup ratios for all ED services ranged by hospital from 1.0 to 12.6 (median, 4.2; interquartile range [IQR], 3.3-5.8); markup ratios for all internal medicine services ranged by hospital from 1.0 to 14.1 (median, 2.0; IQR, 1.7-2.5). The median markup ratio by hospital for ED evaluation and management procedure codes varied between 4.0 and 5.0. Among the most common ED services, laceration repair had the highest median markup ratio (7.0); emergency medicine physician review of a head computed tomographic scan had the greatest interhospital variation (range, 1.6-27.7). Across hospitals, markups in the ED were often substantially higher than those in the internal medicine department for the same services. Higher ED markup ratios were associated with hospital for-profit ownership (median, 5.7; IQR, 4.0-7.1), a greater percentage of uninsured patients seen (median, 5.0; IQR, 3.5-6.7 for ≥20% uninsured), and location (median, 5.3; IQR, 3.8-6.8 for the southeastern United States). Across hospitals, there is wide variation in excess charges on ED services, which are often priced higher than internal medicine services. Our results inform policy efforts to protect uninsured and out-of-network patients from highly variable pricing.

A quality assessment tool for markup-based clinical guidelines.

PubMed

Shalom, Erez; Shahar, Yuval; Taieb-Maimon, Meirav; Lunenfeld, Eitan

2008-11-06

We introduce a tool for quality assessment of procedural and declarative knowledge. We developed this tool for evaluating the specification of mark-up-based clinical GLs. Using this graphical tool, the expert physician and knowledge engineer collaborate to perform scoring, using pre-defined scoring scale, each of the knowledge roles of the mark-ups, comparing it to a gold standard. The tool enables scoring the mark-ups simultaneously at different sites by different users at different locations.

Changes in latent fingerprint examiners' markup between analysis and comparison.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2015-02-01

After the initial analysis of a latent print, an examiner will sometimes revise the assessment during comparison with an exemplar. Changes between analysis and comparison may indicate that the initial analysis of the latent was inadequate, or that confirmation bias may have affected the comparison. 170 volunteer latent print examiners, each randomly assigned 22 pairs of prints from a pool of 320 total pairs, provided detailed markup documenting their interpretations of the prints and the bases for their comparison conclusions. We describe changes in value assessments and markup of features and clarity. When examiners individualized, they almost always added or deleted minutiae (90.3% of individualizations); every examiner revised at least some markups. For inconclusive and exclusion determinations, changes were less common, and features were added more frequently when the image pair was mated (same source). Even when individualizations were based on eight or fewer corresponding minutiae, in most cases some of those minutiae had been added during comparison. One erroneous individualization was observed: the markup changes were notably extreme, and almost all of the corresponding minutiae had been added during comparison. Latents assessed to be of value for exclusion only (VEO) during analysis were often individualized when compared to a mated exemplar (26%); in our previous work, where examiners were not required to provide markup of features, VEO individualizations were much less common (1.8%). Published by Elsevier Ireland Ltd.

Online Tools for Astronomy and Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, B. S.

2005-01-01

Over the past year, the Webnucleo Group at Clemson University has been developing a web site with a number of interactive online tools for astronomy and cosmochemistry applications. The site uses SHP (Simplified Hypertext Preprocessor), which, because of its flexibility, allows us to embed almost any computer language into our web pages. For a description of SHP, please see http://www.joeldenny.com/ At our web site, an internet user may mine large and complex data sets, such as our stellar evolution models, and make graphs or tables of the results. The user may also run some of our detailed nuclear physics and astrophysics codes, such as our nuclear statistical equilibrium code, which is written in fortran and C. Again, the user may make graphs and tables and download the results.