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

, 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 ...

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