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

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

information using tools such as

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding electronic document, documents in a format that is both human-readable and Machine-r ...

and

Java Java is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea (a part of Pacific Ocean) to the north. With a population of 156.9 million people (including Madura) in mid 2024, proje ...

. 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 constrai ...

, 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 ...

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 simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of mol ...

* 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 founded by Geoffrey B. Jeffery, Tim Perdue, and Drew Streib in November 1999. SourceForge provides a centralized software discovery platform, including an online platform for managing and hosting open-source soft ...

. 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 of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the m ...

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 model, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves w ...

Software support

Software importing and exporting a valid CML format * Bioclipse * CDK * JOELib * OpenBabel * Avogadro * XDrawChem * OpenChrom

References

External links

Chemical Markup Language (CML)
This includes the CML Schema, links to tools, documentation, and source code
CML BlogThe original (old) site
{{Document markup languages Markup languages Industry-specific XML-based standards Chemical file formats Cheminformatics Computational chemistry Computer-related introductions in 1999

Versioning

Tools

Software support

See also

References

Further reading

External links