Matml: XML for Information Exchange with Materials Property Data
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
Linking Nwchem and Avogadro with the Syntax and Semantics of Chemical Markup Language Wibe a De Jong1*†, Andrew M Walker2† and Marcus D Hanwell3†
de Jong et al. Journal of Cheminformatics 2013, 5:25 http://www.jcheminf.com/content/5/1/25 RESEARCH ARTICLE Open Access From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language Wibe A de Jong1*†, Andrew M Walker2† and Marcus D Hanwell3† Abstract 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 an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. 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 and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. -
ABBREVIATIONS EBU Technical Review
ABBREVIATIONS EBU Technical Review AbbreviationsLast updated: January 2012 720i 720 lines, interlaced scan ACATS Advisory Committee on Advanced Television 720p/50 High-definition progressively-scanned TV format Systems (USA) of 1280 x 720 pixels at 50 frames per second ACELP (MPEG-4) A Code-Excited Linear Prediction 1080i/25 High-definition interlaced TV format of ACK ACKnowledgement 1920 x 1080 pixels at 25 frames per second, i.e. ACLR Adjacent Channel Leakage Ratio 50 fields (half frames) every second ACM Adaptive Coding and Modulation 1080p/25 High-definition progressively-scanned TV format ACS Adjacent Channel Selectivity of 1920 x 1080 pixels at 25 frames per second ACT Association of Commercial Television in 1080p/50 High-definition progressively-scanned TV format Europe of 1920 x 1080 pixels at 50 frames per second http://www.acte.be 1080p/60 High-definition progressively-scanned TV format ACTS Advanced Communications Technologies and of 1920 x 1080 pixels at 60 frames per second Services AD Analogue-to-Digital AD Anno Domini (after the birth of Jesus of Nazareth) 21CN BT’s 21st Century Network AD Approved Document 2k COFDM transmission mode with around 2000 AD Audio Description carriers ADC Analogue-to-Digital Converter 3DTV 3-Dimension Television ADIP ADress In Pre-groove 3G 3rd Generation mobile communications ADM (ATM) Add/Drop Multiplexer 4G 4th Generation mobile communications ADPCM Adaptive Differential Pulse Code Modulation 3GPP 3rd Generation Partnership Project ADR Automatic Dialogue Replacement 3GPP2 3rd Generation Partnership -
XML for Java Developers G22.3033-002 Course Roadmap
XML for Java Developers G22.3033-002 Session 1 - Main Theme Markup Language Technologies (Part I) Dr. Jean-Claude Franchitti New York University Computer Science Department Courant Institute of Mathematical Sciences 1 Course Roadmap Consider the Spectrum of Applications Architectures Distributed vs. Decentralized Apps + Thick vs. Thin Clients J2EE for eCommerce vs. J2EE/Web Services, JXTA, etc. Learn Specific XML/Java “Patterns” Used for Data/Content Presentation, Data Exchange, and Application Configuration Cover XML/Java Technologies According to their Use in the Various Phases of the Application Development Lifecycle (i.e., Discovery, Design, Development, Deployment, Administration) e.g., Modeling, Configuration Management, Processing, Rendering, Querying, Secure Messaging, etc. Develop XML Applications as Assemblies of Reusable XML- Based Services (Applications of XML + Java Applications) 2 1 Agenda XML Generics Course Logistics, Structure and Objectives History of Meta-Markup Languages XML Applications: Markup Languages XML Information Modeling Applications XML-Based Architectures XML and Java XML Development Tools Summary Class Project Readings Assignment #1a 3 Part I Introduction 4 2 XML Generics XML means eXtensible Markup Language XML expresses the structure of information (i.e., document content) separately from its presentation XSL style sheets are used to convert documents to a presentation format that can be processed by a target presentation device (e.g., HTML in the case of legacy browsers) Need a -
Wireless Application Protocol WAP
Wireless Application Protocol WAP F. Ricci 2008/2009 Content Web and mobility Problems of HTML in the mobile context Wap 1.x Motivations Features Architecture Examples of WML (Wireless Markup Language) pages Wap 2.0 XHTML MP Examples Differences with Wap 1.x Examples World Wide Web and mobility Protocol (HTTP, Hypertext Transfer Protocol) and language (HTML, Hypertext Markup Language) of the Web have not been designed for mobile applications and mobile devices, thus creating many problems! Typical transfer sizes HTTP request: 100-350 byte responses avg. <10 kbyte, header 160 byte, GIF 4.1kByte, JPEG 12.8 kbyte, HTML 5.6 kbyte but also many large files that cannot be ignored The Web is not a file system Web pages are not simple files to download static and dynamic content, interaction with servers via forms, content transformation, push technologies etc. many hyperlinks, automatic loading and reloading, redirecting a single click might have big consequences! HTML and mobile devices HTML designed for computers with “high” performance, color high-resolution display, mouse, hard disk typically, web pages optimized for design, not for communication Mobile devices often only small, low-resolution displays, very limited input interfaces (small touch-pads, soft-keyboards) Additional “features” animated GIF, Java AWT, Frames, ActiveX Controls, Shockwave, movie clips, audio, ... many web pages assume true color, multimedia support, high-resolution and many plug-ins Web pages ignore the heterogeneity of end-systems! -
The Semantics of Chemical Markup Language (CML
Murray-Rust et al. Journal of Cheminformatics 2011, 3:43 http://www.jcheminf.com/content/3/1/43 RESEARCH ARTICLE Open Access The semantics of Chemical Markup Language (CML): dictionaries and conventions Peter Murray-Rust1*, Joe A Townsend1, Sam E Adams1, Weerapong Phadungsukanan2 and Jens Thomas3 Abstract 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. Introduction semantics through dictionaries. These have ranged from From an early stage, Chemical Markup Language (CML) a formally controlled ontology (ChemAxiom [2]) which was designed so that it could accommodate an indefi- is consistent with OWL2.0 [3] and the biosciences’ nitely large amount of chemical and related concepts. Open Biological and Biomedical Ontologies (OBO)[4] This objective has been achieved by developing a dic- framework, to uncontrolled folksonomy-like tagging. tionary mechanism where many of the semantics are Although we have implemented ChemAxiom and it is added not through hard-coded elements and attributes part of the bioscientists’ description of chemistry, we but by linking to semantic dictionaries. CML has a regard it as too challenging for the current practice of number of objects and object containers which are chemistry and unnecessary for its communication. -
Guia Internet Para Periodistas.Pdf
Indice general Presentación ................................................................................................................................... 9 Introducción ................................................................................................................................. 11 Capítulo 1. Sociedad de la información e Internet. Isabel Fernández Morales ......................... 13 1.1 Sociedad de la información .................................................................................................. 13 1.2 Historia de Internet .............................................................................................................. 15 1.3 Tecnologías de acceso .......................................................................................................... 18 1.4 Tipo de acceso ..................................................................................................................... 18 1.5 Terminales de acceso ........................................................................................................... 20 1.6 Servidores ............................................................................................................................. 20 1.6.1 Servicios de web hosting ............................................................................................... 21 1.7 Proveedores de acceso ......................................................................................................... 22 1.8 Dominios ............................................................................................................................. -
Archive and Compressed [Edit]
Archive and compressed [edit] Main article: List of archive formats • .?Q? – files compressed by the SQ program • 7z – 7-Zip compressed file • AAC – Advanced Audio Coding • ace – ACE compressed file • ALZ – ALZip compressed file • APK – Applications installable on Android • AT3 – Sony's UMD Data compression • .bke – BackupEarth.com Data compression • ARC • ARJ – ARJ compressed file • BA – Scifer Archive (.ba), Scifer External Archive Type • big – Special file compression format used by Electronic Arts for compressing the data for many of EA's games • BIK (.bik) – Bink Video file. A video compression system developed by RAD Game Tools • BKF (.bkf) – Microsoft backup created by NTBACKUP.EXE • bzip2 – (.bz2) • bld - Skyscraper Simulator Building • c4 – JEDMICS image files, a DOD system • cab – Microsoft Cabinet • cals – JEDMICS image files, a DOD system • cpt/sea – Compact Pro (Macintosh) • DAA – Closed-format, Windows-only compressed disk image • deb – Debian Linux install package • DMG – an Apple compressed/encrypted format • DDZ – a file which can only be used by the "daydreamer engine" created by "fever-dreamer", a program similar to RAGS, it's mainly used to make somewhat short games. • DPE – Package of AVE documents made with Aquafadas digital publishing tools. • EEA – An encrypted CAB, ostensibly for protecting email attachments • .egg – Alzip Egg Edition compressed file • EGT (.egt) – EGT Universal Document also used to create compressed cabinet files replaces .ecab • ECAB (.ECAB, .ezip) – EGT Compressed Folder used in advanced systems to compress entire system folders, replaced by EGT Universal Document • ESS (.ess) – EGT SmartSense File, detects files compressed using the EGT compression system. • GHO (.gho, .ghs) – Norton Ghost • gzip (.gz) – Compressed file • IPG (.ipg) – Format in which Apple Inc. -
Forcepoint DLP Supported File Formats and Size Limits
Forcepoint DLP Supported File Formats and Size Limits Supported File Formats and Size Limits | Forcepoint DLP | v8.8.1 This article provides a list of the file formats that can be analyzed by Forcepoint DLP, file formats from which content and meta data can be extracted, and the file size limits for network, endpoint, and discovery functions. See: ● Supported File Formats ● File Size Limits © 2021 Forcepoint LLC Supported File Formats Supported File Formats and Size Limits | Forcepoint DLP | v8.8.1 The following tables lists the file formats supported by Forcepoint DLP. File formats are in alphabetical order by format group. ● Archive For mats, page 3 ● Backup Formats, page 7 ● Business Intelligence (BI) and Analysis Formats, page 8 ● Computer-Aided Design Formats, page 9 ● Cryptography Formats, page 12 ● Database Formats, page 14 ● Desktop publishing formats, page 16 ● eBook/Audio book formats, page 17 ● Executable formats, page 18 ● Font formats, page 20 ● Graphics formats - general, page 21 ● Graphics formats - vector graphics, page 26 ● Library formats, page 29 ● Log formats, page 30 ● Mail formats, page 31 ● Multimedia formats, page 32 ● Object formats, page 37 ● Presentation formats, page 38 ● Project management formats, page 40 ● Spreadsheet formats, page 41 ● Text and markup formats, page 43 ● Word processing formats, page 45 ● Miscellaneous formats, page 53 Supported file formats are added and updated frequently. Key to support tables Symbol Description Y The format is supported N The format is not supported P Partial metadata -
Understanding
Implementing UBL Mark Crawford UBL Vice Chair XML 2003 9 December 2003 Why Are We Talking About UBL • UBL fulfils the promise of XML for business by defining a standard cross-industry vocabulary • UBL is the ebXML missing link • UBL plus ebXML enables the next generation of eBusiness exchanges – Cheaper, easier, Internet-ready – Extends benefits of EDI to small businesses – Fits existing legal and trade concepts – Allows re-use of data • UBL can provide the XML payload for a wide variety of other web-based business frameworks Overview 1 What and Why of UBL 2 The Design of UBL ebXML Core Components Naming and Design Rules Document Engineering Customizing UBL 3 The Content of UBL 1.0 What is Normative What is non-Normative Availability 4 Making UBL Happen 5 UBL Phase 2 6 Summary The promise of XML for e-business • Plug ‘n’ play electronic commerce – Spontaneous trade – No custom programming • Ubiquity on the Internet – Dirt-cheap tools – Complete platform independence – Enable true global market availability • Enable universal interoperability – Abandon existing EDI systems – Handle both "publication" document types and "transactional" documents Goals for Successful eBusiness Services • Web-enable existing fax- and paper-based business practices • Allow businesses to upgrade at their own pace • Preserve the existing investment in electronic business exchanges • Integrate small and medium-size businesses into existing electronic data exchange-based supply chains The standardization of XML business documents is the easiest way to accomplish -
An XML Format for Proteomics Database to Accelerate Collaboration Among Researchers
AO HUPO workshop in Tsukuba (Dec. 19, 2002) An XML Format For Proteomics Database to Accelerate Collaboration Among Researchers HUP-ML: Human Proteome Markup Language K. Kamijo, H. Mizuguchi, A. Kenmochi, M. Sato, Y. Takaki and A. Tsugita Proteomics Res. Center, NEC Corp. 1 Overview (HUP-ML) z Introduction z XML features z XMLs in life science z HUP-ML concept z Example of HUP-ML z Details of HUP-ML z Demonstration of “HUP-ML Editor” 2 Introduction z Download entries from public DBs as a flat-file z easy for a person to read z different formats for every DB z sometimes needs special access methods and special applications for each format z Needs machine-readable formats for software tools z To boost studies by exchanging data among researchers Activates standardization 3 XML format z XML (eXtensible Markup Language) W3C: World Wide Web Consortium (inception in 1996) Attribute Key Value Example Element Start Tag <tag_element_source attribute_growth=“8 weeks”> rice leaf </tag_element_source> End Tag z Highly readable for machine and person z Can represent information hierarchy and relationships z Details can be added right away z Convenient for exchanging data z Easy to translate to other formats 4 z Logical-check by a Document Type Definition (DTD) Overview (HUP-ML) z Introduction z XML features z XMLs in life science z HUP-ML concept z Example of HUP-ML z Details of HUP-ML z Demonstration of “HUP-ML Editor” 5 XML features z Exchangeable z Inter-operability: z OS (Operating System): Windows, Linux, etc. z Software Development Languages -
Wap, Xhtml and Android
WAP, XHTML AND ANDROID Jaume Barceló University Carlos III of Madrid Antonio de la Oliva Ruben cuevas Service Engineering Laboratory Ignacio soto BACK IN 1999, • Mobile and Internet communications were separate worlds • Nokia 7110, first mobile phone with a WAP browser. • WAP: Wireless Application Protocol. • Extra-simplified access to the Internet, due to terminal limitations and limited available bandwidth. SMALL LIMITATIONS, • Extremely limited bandwidth • SMS • Circuit-switching • Wait-and-pay • A substantial increase thanks to GPRS (2.5G) ~ 56kbps • Memory and processor limitations • Low resolution monochrome screen • No mouse, 15-keys keyboard WAP PROTOCOL STACK Internet Protocol Stack HTML Wireless Application Environment (WAE) JavaScript 1. Wireless Session Layer (WSP) HTTP 2. Wireless Transaction Protocol (WTP) TLS-SSL 3. Wireless Transport Layer Security (WTLS) 4. Wireless Datagram Protocol (WDP) TCP/IP UDP/IP Bearers: SMS USSD CSD CDMA IS-136 CDPD Etc.. A GW WAS REQUIRED WIRELESS APPLICATION ENVIRONMENT In WAP 1.X Wireless Markup Language (WML) Relies on a card/desk paradigm WMLScript WML EXAMPLE <?xml version="1.0"?> <!DOCTYPE wml PUBLIC "-//WAPFORUM//DTD WML 1.1//EN" "http://www.wapforum.org/DTD/wml_1.1.xml"> <wml> <card id="card1" title="Tutorial"> <do type="accept" label="Answer"> <go href="#card2"/> </do> <p><select name="name"> <option value="HTML">HTML Tutorial</option> <option value="XML">XML Tutorial</option> <option value="WAP">WAP Tutorial</option> </select></p> </card> <card id="card2" title="Answer"> <p>You