Chemical Markup Language (ChemML or CML) is an approach to managing
molecular information using tools such as
XML
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable ...
and
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...
. It was the first domain specific implementation based strictly on
XML
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable ...
, first based on a
DTD and later on an
XML Schema
An XML schema is a description of a type of XML document, typically expressed in terms of constraints on the structure and content of documents of that type, above and beyond the basic syntactical constraints imposed by XML itself. These constra ...
, the most robust and widely used system for precise information management in many areas. It has been developed over more than a decade by
Murray-Rust,
Rzepa and others and has been tested in many areas and on a variety of machines.
Chemical information is traditionally stored in many different file types which inhibit reuse of the documents. CML uses XML's portability to help CML developers and chemists design interoperable documents. There are a number of tools that can generate, process and view CML documents. Publishers can distribute chemistry within XML documents by using CML, e.g. in
RSS
RSS ( RDF Site Summary or Really Simple Syndication) is a web feed that allows users and applications to access updates to websites in a standardized, computer-readable format. Subscribing to RSS feeds can allow a user to keep track of many di ...
documents.
CML is capable of supporting a wide range of chemical concepts including:
* molecules
* reactions
* spectra and analytical data
*
computational chemistry
* chemical crystallography and materials
Details of CML and points currently under discussion are now posted on the CML Blog.
Versioning
Versions of the schema are available at
SourceForge
SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirroring ...
. As of April 2012, the latest frozen schema is CML v2.4. Some constructs in CML v1 are now deprecated.
Tools
JUMBO began life as the Java Universal Molecular Browser for Objects but is now a Java library that supports validation, reading and writing of CML as well as conversion of several legacy formats to CML and, for example, a reaction in CML to an animated SVG representation of the reaction. JUMBO has evolved into an extensive Java library, CMLDOM, supporting all elements in the schema. Although JUMBO used to be a browser, the preferred approach is to use the Open Source tools
Jmol
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry.
It is written in the ...
and
JChemPaint, some of which use alternative CML libraries.
See
Blue Obelisk
Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obeli ...
.
See also
*
List of document markup languages
The following is a list of document markup languages. You may also find the List of markup languages of interest.
Well-known document markup languages
* HyperText Markup Language (HTML) – the original markup language that was defined as a part o ...
*
Comparison of document markup languages The following tables compare general and technical information for a number of document markup languages. Please see the individual markup languages' articles for further information.
General information
Basic general information about the marku ...
* Software importing and exporting a valid CML format
**
Bioclipse
**
CDK
**
JOELib
JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. ...
**
OpenBabel
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats.
About
Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular model ...
**
Avogadro
*
Joint Committee on Atomic and Molecular Physical Data The Joint Committee on Atomic and Molecular Physical Data (JCAMP) defined several JCAMP-DX (JCAMP-data exchange) file formats in chemistry. IUPAC
The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of ...
(another well-known standard, especially for spectroscopic data)
*
Blue Obelisk
Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obeli ...
community for Open Source chemical software
*
MathML
Mathematical Markup Language (MathML) is a mathematical markup language, an application of XML for describing mathematical notations and capturing both its structure and content. It aims at integrating mathematical formulae into World Wide W ...
PCML-- an unofficial successor used i
DeepMatter's DigitalGlasswareplatform
References
Further reading
*
*
External links
This includes the CML Schema, links to tools, documentation, and source code
CML BlogThe original (old) siteThe Jmol Browser's site
{{Document markup languages
Markup languages
Industry-specific XML-based standards
Chemical file formats
Computer-related introductions in 1999