Specialized Content Markup Languages
(An Expert Handlers SIG Reference)
- 1 Specialized Content Markup Languages(An Expert Handlers SIG Reference)
Alphabetic Index of Specialized Content Markup Languages
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Biological/Biochemical and Genomic Markup Languages
- CellML :
- A repository of several hundred biological models encoded into CellML  can be found on the CellML community's CellML Repository. These models are actively undergoing a curation process aiming to provide annotations with biological ontologies such as Gene Ontology and to validate the models against standards of unit balance and biophysical constrains such as conservation of mass, charge, energy. etc.
- GEDML: Geneological Data Markup Language 
- GEDML is used to encode geneological data sets in XML.
- GEDML Document Type Definition (DTD) 
- GEML or GeneXML: Gene Expression Markup Language 
- GEML is an open-standard XML format for DNA microarray and gene expression data, developed by Rosetta Biosoftware, Inc.
- EMBL Nucleotide Database 
- management and distribution of data on macromolecular structures 
- ArrayExpress: for gene expression data 
- Ensembl: provides up to date completed metazoic genomes and the best possible automatic annotation 
- IntAct: freely available, open source database system and analysis tools for protein interaction data 
Chemical/Chemistry Markup Languages
Geographic and Topographic Markup Languages
- GML: Geography Markup Language 
- The Geography Markup Language (GML) is an XML encoding for the transport and storage of geographic information, including both the spatial and non-spatial properties of geographic features. Developed by the OpenGIS Consortium.
- GML Schema & Documentation 
- LandXML: Land Extensible Markup Language 
- Developed by the LandXML Organization, the LandXML schema facilitates the exchange of data created during the Land Planning, Civil Engineering and Land Survey process.
Mathematical Markup Languages
- GDML: Geometry Description Markup Language 
- The Geometry Description Markup Language (GDML), originally developed at CERN, is an application-indepedent geometry description format based on XML. It can be used as the primary geometry implementation language as well as providing a geometry data exchange format for existing applications. The workpackage consists of the GDML Schema part, which is a fully self-consistent definition of the GDML syntax and the GDML I/O part which provides means for writing out and reading in GDML files. The GDML Schema does not depend in any way on the GDML I/O packages. In particular, new extensions to the GDML I/O packages can be implemented (interfaces to new application, like for instance visualisation, editors, etc.), while the GDML Schema definition remains unchanged. At the present moment, there exist two toolkit bindings for GDML, the Geant4 binding and the ROOT binding (integrated within the ROOT framework). Both bindings support the GDML importation (reading GDML files) as well as the exportation (writing out GDML files).
- Example geometry file markedup using GDML 
- Mathematical Markup Language (MathML) 2.0 (Second Edition) 
- Mathematical Markup Language, MathML is an XML application  for describing mathematical notation and capturing both its structure and content. The goal of MathML is to enable mathematics to be served, received, and processed on the World Wide Web, just as HTML has enabled this functionality for text.
- related resource: A MathML for CSS profile  Note: the current profile is intended to be subset of MathML 3.0  that could be used to capture structure of mathematical formulae in the way suitable for further CSS formatting. This profile is expected to facilitate adoption of MathML in web browsers and CSS formatters, allowing them to reuse the existing CSS visual formatting model, enhanced with a few mathematics oriented extensions, for rendering of layouts schemata of presentational MathML. Development of the CSS profile is assumed to be coordinated with ongoing work on CSS3 and may require a limited set of new properties to be added to existing CSS3 modules. Note, that, in connection with the need for this profile, that the CSS2 specification, Level 2.0  was developed and refined at about the same time as the first MathML specification . Now new versions of both MathML and CSS are being created. This profile is thus part of the ongoing effort to realize the synergy that W3C Recommendations offer to the Web.
Musical Markup Languages
- FLOWML: Flow Markup Language 
- FlowML is a format for storing audio synthesis diagrams, as used in various software synthesizers.
- MusicXML: eXtensible Musical Markup Language :
- MusicXML was created to provide an internet-friendly method of publishing musical scores, enabling musicians and music fans to get more out of their online music. MusicXML 2.0 files serve the same role for interactive sheet music that MP3 files serve for recorded music. The MusicXML format represents common Western musical notation from the 17th century onward. It lets you distribute interactive sheet music online, and to use sheet music files with a wide variety of musical applications. The MusicXML format is open for use by anyone under a royalty-free license, and is supported by over 80 applications
- MusicXML Schema 
- GDML: Generalized Dynamic Markup Language 
- The Generalized Dynamic Markup Language (gdml) is designed to provide A standardized method of embedding customized and dynamically generated Web content into HTML-based templates. This makes it possible for the HTML designer to control the look and feel of the site and alter critical components such as site navigation without the expensive intervention of the programmer.
- Introduction to Generalized Dynamic Markup Language (GDML) 
- HEML: Historical Event Markup and Linking 
- The Historical Event Markup and Linking project explores XML-related technologies to develop a set of text markup and transformation tools that are useful to historians world-wide.
- HEML Schemata 
- IML: Instrument Markup Language  & ICML Instrument Control Markup Language
- The Instrument Markup Language (IML) is designed to be a very general and highly extensible framework that applies to virtually any kind of instrument that can be controlled by a computer. Developed at the NASA Goddard Space Flight Center (GSFC).
- IML Schema (XSD) 
- IML/ICML Shared Schema (XSD) 
- International Press Telecommunications Council (IPTC) family of languages 
- RixML Specification (Current Schema) 
- RixML FAQ 
- RixML Examples 
- RixML Scenarios 
- Additional RixML Resources 
As Yet Unclassified
- HumanML: Human Markup Language 
- Developed by OASIS , HumanML is designed to represent human characteristics through XML. The stated aim of HumanML is to enhance the fidelity of human communication.
- HumanML is an XML Schema and RDF Schema specification, containing sets of modules which frame and embed contextual human characteristics including physical, cultural, social, kinesic, psychological, and intentional features within conveyed information. Other efforts include messaging, style, alternate schemas, constraint mechanisms, object models, and repository systems, which will address the overall concerns of both representing and amalgamating human information within data. Examples of human characteristics include emotions, physical descriptors, proxemics, kinesics, haptics, intentions, and attitude. Applications of HumanML include agents of various types, AI systems, virtual reality, psychotherapy, online negotiations, facilitations, dialogue, and conflict resolution systems.
- HumanML Schema (XSD)