Chemical Markup Language - AbsoluteAstronomy.com

CML is an approach to managing molecular information using tools such as XML

XML

Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....

and Java. It was the first domain specific implementation based strictly on XML

XML

, first based on a DTD

Document Type Definition

Document Type Definition is a set of markup declarations that define a document type for SGML-family markup languages...

and later on XML Schema, 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

Peter Murray-Rust

Peter Murray-Rust is a contemporary chemist born in Guildford in 1941.He was educated at Bootham School and Balliol College, Oxford. After obtaining a D.Phil he became lecturer in chemistry at the University of Stirling and was first warden of Andrew Stewart Hall of Residence...

, Rzepa

Henry Rzepa

Henry S. Rzepa is a contemporary computational organic chemist. He was born in London in 1950, was educated at Wandsworth Comprehensive School, and then entered the chemistry department at Imperial College London where he graduated in 1971. Following a Ph.D...

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 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

The latest versions of the schema are available at Sourceforge. The latest frozen schema is CML2.4. A number of constructs in CML1 were DTD-based and are now deprecated so users should consider using CML v2.

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

Jmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...

and JChemPaint

JChemPaint

JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems...

, some of which use alternative CML libraries. See Blue Obelisk

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...

External links

Chemical Markup Language (CML) This includes the CML Schema, links to tools, documentation, and source code
Discussion list
CML Blog
The original (old) site
The Jmol Browser's site

The source of this article is wikipedia, the free encyclopedia. The text of this article is licensed under the GFDL.

Versioning

Tools

See also

External links