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

Peter Murray-Rust, Joe A Townsend, Sam E Adams, Weerapong Phadungsukanan, Jens Thomas
2011 Journal of Cheminformatics  
Elements in a document link to conventions, dictionaries and units through attributes.  ...  The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation).  ...  Introduction From an early stage, Chemical Markup Language (CML) was designed so that it could accommodate an indefinitely large amount of chemical and related concepts.  ... 
doi:10.1186/1758-2946-3-43 pmid:21999509 pmcid:PMC3206453 fatcat:fa2nf5bntbahxgcnzslex4nphu

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

Weerapong Phadungsukanan, Markus Kraft, Joe A Townsend, Peter Murray-Rust
2012 Journal of Cheminformatics  
The eXtensible Markup Language [6] (XML) is usually selected for storing data due to its universality and extensibility for both simple and complex data.  ...  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.  ...  For chemistry applications, the Chemical Markup Language (CML) [7] [8] [9] [10] has been developed based on the XML standard in order to provide the semantics for chemical data.  ... 
doi:10.1186/1758-2946-4-15 pmid:22870956 pmcid:PMC3434037 fatcat:vcse664chnbuxpuzrh2ft2ttia

Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators

Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, Egon L. Willighagen
2004 Journal of chemical information and computer sciences  
XML is itself a specification for creating families and subfamilies of more specific markup languages.  ...  INTRODUCTION There is increasing recognition that the World Wide Web has vast untapped potential as an infrastructure for structured data interchange rather than just being a medium for delivering documents  ... 
doi:10.1021/ci034244p pmid:15032525 fatcat:wmbuzsqxgjbo3lfq43evx5w2yq

Curl: a language for web content

Steve Ward, Mat Hostetter
2003 International Journal of Web Engineering and Technology  
The approach described maps conventional markup tags to underlying, more general programming constructs, and provides local extensibility of the markup language by addition of programmed objects, procedures  ...  Key words and phrases: web language, programming language design, content delivery, incremental compilation, extensible language design, markup language Biographical Notes: Steve Ward is a Professor of  ...  Major contributors to that effort include David Kranz, who implemented the majority of the MIT prototype system [10] , and Chris Terman who was a principal contributor to its architectural decisions.  ... 
doi:10.1504/ijwet.2003.003259 fatcat:lvnv5tmg5bhgbckqs6slltjaka

Gas Hydrate Markup Language: Laboratory Data

Tom Smith, John Ripmeester, Dendy Sloan, Tsutomu Uchida
2007 Data Science Journal  
Laboratory Hydrate Data is one of the three constituent modules comprising the XML based Gas Hydrate Markup Language (a.k.a.  ...  This module describes the characteristics of natural and synthetic gas hydrates as they pertain to data acquired via analysis within a laboratory environment.  ...  CODATA contributed over the course of this project to support travel costs.  ... 
doi:10.2481/dsj.6.gh18 fatcat:uxzirblxjjhpvfqq5u5eyryxty

CIF: the computer language of crystallography

I. David Brown, Brian McMahon
2002 Acta Crystallographica Section B Structural Science  
The Crystallographic Information File (CIF) was adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information.  ...  Future extension of the standard to include implementation of methods will allow CIF to exploit the potential of advanced information-handling software.  ...  We wish to acknowledge the efforts of all the people, too numerous to name, who have contributed to the work described in this paper.  ... 
doi:10.1107/s0108768102003464 pmid:12037350 fatcat:nej4auk6iva57e66r5gsjbvyta

The biology Petri net markup language

Ming Chen, Andreas Freier, Jacob Köhler, Alexander Rüegg
2002 Entwicklungsmethoden für Informationssysteme und deren Anwendung: Fachtagung  
In this paper a proposal for the Biology Petri Net Markup Language (BioPNML) is presented.  ...  BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets.  ...  Authors give particular thanks to Dr. S. Philippi for useful suggestions. We would like to thank the anonymous referee for his/her valuable comments and suggestions.  ... 
dblp:conf/emisa/ChenFKR02 fatcat:hdwx24cokbbw5p7zwyebyqyfym

Compatibility of XML Language Versions [chapter]

Daniel Dui, Wolfgang Emmerich
2003 Lecture Notes in Computer Science  
In addition to internal consistency of the language definition, also consistency between the language and its instance XML documents needs to be preserved when evolving the language definition.  ...  We propose to evaluate the method by using different versions of the Financial products Markup Language (FpML) in whose definition we participate.  ...  version and configuration managements challenges of FpML in particular and XML languages in general.  ... 
doi:10.1007/3-540-39195-9_11 fatcat:jz7s77kcnvfcncj63hiiz4mxq4

STMML. A markup language for scientific, technical and medical publishing

Peter Murray-Rust, Henry S. Rzepa
2002 Data Science Journal  
STMML is an XML-based markup language covering many generic aspects of scientific information. It has been developed as a re-usable core for more specific markup languages.  ...  We have shown how STMML as an XML-based markup language can cover many generic aspects of scientific information and how it has been developed as a re-usable core for more specific markup languages.  ...  For example we have developed a language termed Chemical Markup Language or CML (Murray-Rust & Rzepa, 1999; Murray-Rust & Rzepa, 2001) to manage chemical information, especially molecules.  ... 
doi:10.2481/dsj.1.128 fatcat:bzorruw4g5aarkysjjq27m7dwa

A Query Language and User Interface for XML Information Retrieval [chapter]

Norbert Fuhr, Kai Großjohann, Sascha Kriewel
2003 Lecture Notes in Computer Science  
Since XML supports logical markup of texts both at the macro level (structuring markup for chapter, section, paragraph and so on) and the micro level (e.g., MathML for mathematical formulas, CML for chemical  ...  Introduction As XML is about to become the standard format for structured documents, there is an increasing need for appropriate information retrieval (IR) methods.  ... 
doi:10.1007/978-3-540-45194-5_4 fatcat:zlrpowtkyrfxxlifivysrmotxu

Geometry Description Markup Language for Physics Simulation and Analysis Applications

R. Chytracek, J. Mccormick, W. Pokorski, G. Santin
2006 IEEE Transactions on Nuclear Science  
The Geometry Description Markup Language (GDML) is a specialized XML-based language designed as an application-independent persistent format for describing the geometries of detectors associated with physics  ...  It serves to implement "geometry trees" which correspond to the hierarchy of volumes a detector geometry can be composed of, and to allow to identify the position of individual solids, as well as to describe  ...  The Geometry Description Markup Language (GDML) has been developed as an application of XML. This option provides a simple reading and writing mechanism, as well as extensibility.  ... 
doi:10.1109/tns.2006.881062 fatcat:2hgfuy4razezpmd6tedi4wa6ka

Systems biology graphical notation markup language (SBGNML) version 0.3

Frank T Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L Blinov, Augustin Luna
2020 Journal of Integrative Bioinformatics  
This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and  ...  SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language.  ...  The Class is an enumeration of values used to specify what type a Glyph is encoding. 1 The possible values are unspecified entity, simple chemical, macromolecule, nucleic acid feature, 2 simple chemical  ... 
doi:10.1515/jib-2020-0016 pmid:32568733 fatcat:6qacc7kmnbgqjb527bxuqh6l7y

Modeling Hydrates and the Gas Hydrate Markup Language

Weihua Wang, George Moridis, Runqiang Wang, Yun Xiao, Jianhui Li
2007 Data Science Journal  
At present, metadata (Markup Language) is recognized as one of the most efficient ways to facilitate data management, storage, integration, exchange, discovery and retrieval.  ...  Therefore the CODATA Gas Hydrate Data Task Group proposed and specified Gas Hydrate Markup Language (GHML) as an extensible conceptual metadata model to characterize the features of data on gas hydrate  ...  During the development of this part, we consulted many other international metadata standards (Markup Languages) that provided good references to structure design, naming conventions, annotation format  ... 
doi:10.2481/dsj.6.gh25 fatcat:lv5ygy3tore4vjzrpnzmngssba

Book Review: The ABCs of XML: The Librarian's Guide to the eXtensible Markup Language

Margaret Rohdy, Thomas P. Turner
2000 Library resources & technical services  
what advantages there are in using a powerful markup language.  ...  The eXtensible Markup (XML) has received attention as a method to rev- Language olutionize electronic data interchange, data organization, and information retrieval.  ... 
doi:10.5860/lrts.44n4.214 fatcat:nja7njpdvjcope3d37z7oxq2my

Using the Extensible Markup Language (XML) As a Medium for Data Exchange

Meg Murray
2002 Communications of the Association for Information Systems  
The eXtensible Markup Language (XML) was introduced to meet this challenge by providing a standardized way to exchange data.  ...  XML will evolve as its structure, its strengths, its weaknesses, and how it can be used more effectively are better understood.  ...  XML is a highly structured markup language, meaning it requires users to follow its rules explicitly. The foremost rule of XML is that it must be well-formed.  ... 
doi:10.17705/1cais.00907 fatcat:teqdnajt6vdxrhpygaubuqwu4m
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