Specialized Content Markup Languages (An Expert Handlers SIG Reference)

• 1 Specialized Content Markup Languages(An Expert Handlers SIG Reference)
  • 1.1 Biological/Biochemical and Genomic Markup Languages
  • 1.2 Chemical/Chemistry Markup Languages
  • 1.3 Geographic and Topographic Markup Languages
  • 1.4 Mathematical Markup Languages
  • 1.5 Musical Markup Languages
  • 1.6 XML-Wrappers
  • 1.7 As Yet Unclassified

CellML | CML | FLOWML | GML | GBXML | GDML | GDML | GEML | GIML | HEML | HumanML | IML | IPTC | LandML | MAGE | MathML | MIRIAM | MSAML | MusicXML | NewsML | RedBook | RixML | SPDML | SBML | SBO

Additions, suggestions, and corrections to this list are welcome. Please use this document's Discussion page to do so. Thank you.

• 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.
• GEML Document Type Definition (DTD)
• GIML: Gastro-Intestinal Markup Language
• GIML, the Gastro-Intestinal Markup Language</strong> was originally developed at MIT
• GIML Schema (XSD)
• GeneOntology Markup
• The goal of the Gene Ontology Consortium is to produce a dynamic controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing

.

• GeneOntology Markup Documentation
• MAGE: MicroArray and Gene Expression:
• A standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems. MAGE works within the Object Management Group (OMG). MAGE is working on a data exchange model (MAGE-OM: Microarray Gene Expression - Object Model and a data exchange format, MAGE-ML: Microarray Gene Expression - Markup Language) for microarray expression experiments. There is also a MAGE-TAB: the currently recommended best practice approach.
  
  
• MIRIAM: Minimal Information Requested In the Annotation of biochemical Models
• An effort to standardize the annotation and curation process of quantitative models of biological systems. The goal of the project, initiated by the BioModels.net effort, is to produce a set of guidelines suitable for use with any structured format for computational models, in order to allow different groups to collaborate on annotating and curating computational models in biology
• MSAML: Multiple Sequence Alignments in XML
• MSAML is a set of XML compliant markup components for describing multiple sequence alignments, such as amino acids and nucleic acid sequences. Developed by the National Research Coucil of Canada.
• MSAML Document Type Definition (DTD)
• Systems Biology Markup Language (SBML):
• SBML is a machine-readable language, derived from XML, for representing models of biochemical reaction networks. SBML can represent metabolic networks, cell-signaling pathways, regulatory networks, and other kinds of systems studied in systems biology. As of June 2006, more than 100 software systems support SBML. An up-to-date list can be found at sbml.org.
  
  
• Systems Biology Ontology (SBO):
• The goal of SBO is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems biology, especially in the context of computational modeling. SBML Level 2 Version 2, provides a mechanism to annotate model components with SBO terms, therefore increasing the semantics of the model beyond the sole topology of interaction and mathematical expression.

SBO test documents/suites: * 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

• CML: Chemical Markup Language
• Peer-Reviewed publications relating to CML
• CML Schemas

• 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.

LandXML-1.2: Schema (ratified 2008-08-15) * LandXML 1.2 Data Diagram

• LandXML 1.2 Schema (XSD)
• Spiral Curve Definition Document
• LandXML SDK 1.2 (zipped archive) * SPDML: Space Physics Data Markup Language
• Developed by the Johns Hopkins Advanced Physics The Space Physics Data Markup Language (SPDML) is being developed using XML to provide a standard method for expressing Space Physics data sets. SPDML is being utilized in a prototype system to provide a standard method of data querying enabling multi-instrument comparisons to Thermosphere, Ionosphere, Mesosphere, Energetics and Dynamics (TIMED) data and tracing the Sun-Earth connection. SPDML describes: 1) the structure; 2) the semantics; and 3) the content of any space physics data set in any data format. This allows the construction of metadata from existing data sets in both standard (NetCDF, CDF, ASCII, etc.) formats and mission specific formats to be processed. Commercial off-the-shelf search engines can then be used to discover and access multiple distributed scientific resources, providing easy cataloging and retrieval of Space Physics data as well as providing a multi-instrument comparison to TIMED data.
• SPDML Examples

• 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.

• 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
  1. News Exchange Standards (one of which is NewsML);
  2. NewsCodes;
  3. Photo Metadata * NewsML

NewsML is a structural framework for news, a wrapper, based on Extensible Markup Language (XML) for support of the representation of electronic news items. It allows for the provision of multiple representations of the same information, and handles arbitrary mixtures of media types, formats, languages and encodings. NewsML is part of the International Press Telecommunications Council (ITPC) family of languages, which cover: News Exchange Standards (one of which is NewsML), NewsCodes, and Photo Metadata. * NewsML 1

• Introduction to NewsML
• NewsML Documentation
• NewsML Examples
• Who's Using NewsML?
• NewsML 1 Users Forum
• NewsML-G2
• Introduction to NewsML-G2
• NewsML-G2 Documentation
• NewsML-G2 Examples
• Who's Using NewsML-G2?
• NewsML-G2 Users Forum * RedBook:
• An Electronic Filing System (EFS) based upon a standard called Red Book, developed by the US Patent and Trademark office. The Red Book standard helps define and validate documents intended for trademark and patent submission.
• Research Information eXchange Markup Language (RixML):

The RixML standard was created by the RIXML.org organization to enable investment and financial firms to share research documents between firms, such as morning calls, company and stock reports, etc. * RixML Specification (Current Schema)

• RixML FAQ
• RixML Examples
• RixML Scenarios
• Additional RixML Resources
  

• 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)

• Expert Handlers References Index
• Expert Handlers Use Cases Drafts Index
• Expert Handlers Special Interest Group's main page
• Open Accessibility (A11y) Working Group's front page