Chemical Markup Language (ChemML or CML) is an approach to managing

molecular A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...

information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on an 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,

Rzepa Rzepa () is a Polish surname. Meaning and origin The name derives from ''rzepa'', a Polish word meaning turnip. Notable people Notable people with this name include: * Henry Rzepa (born 1950), British chemist * Miroslaw Rzepa (born 1968), Polish ...

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 Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of m ...

* 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. 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 and

JChemPaint JChemPaint is computer software, a molecule editor and file viewer for chemical structures using 2D computer graphics.''JChemPaint - Using the Collaborative Forces of the Internet to Develop a Free Editor for 2D Chemical Structures'', Stefan Krau ...

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

References

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

Versioning

Tools

See also

References

Further reading

External links