CHEMICAL MARKUP LANGUAGE (CHEMML or CML) is an approach to managing
molecular 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
and others and has been tested in many areas and on a variety of
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
* 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.
* 1 Versioning
* 2 Tools
* 3 See also
* 4 References
* 5 Further reading
* 6 External links
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.
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
JChemPaint , some of which use alternative CML
Blue Obelisk .
List of document markup languages
Comparison of document markup languages
Comparison of document markup languages
* Software importing and exporting a valid CML format
* Joint Committee on Atomic and
Molecular Physical Data (another
well-known standard, especially for spectroscopic data)
Blue Obelisk community for Open Source chemical software
* ^ Murray-Rust, Peter; Rzepa, Henry S (2011). "CML: Evolution and
Journal of Cheminformatics . 3 (1): 44. doi
* ^ Murray-Rust, P.; Rzepa, H. S. (1999), "Chemical Markup, XML,
and the Worldwide Web. 1. Basic Principles", J. Chem. Inf. Comput.
Sci. , 39 (6): 928–942, doi :10.1021/ci990052b
* ^ Murray-Rust, P.; Rzepa, H. S. (2003), "Chemical Markup,
the World Wide Web. 4. CML Schema",
J. Chem. Inf. Comput. Sci. , 43
(3): 757–772, doi :10.1021/ci0256541
* ^ Gkoutos, G. V.; Murray-Rust, P.; Rzepa, S.; Wright, M. (2001),
"Chemical Markup, XML, and the World-Wide Web. 3. Toward a Signed
Semantic Chemical Web of Trust",
J. Chem. Inf. Comput. Sci. , 41 (5):
1124–1130, doi :10.1021/ci000406v
* ^ Holliday, G. L.; Murray-Rust, P.; Rzepa, H. S. (2006),
XML and the World Wide Web. Part 6. CMLReact; An XML
Vocabulary for Chemical Reactions",
J. Chem. Inf. Model. , 46 (1):
145–157, doi :10.1021/ci0502698
* ^ Kuhn, S.; Helmus, T.; Lancashire,, R. J.; Murray-Rust, P.;
Rzepa, H. S.; Steinbeck, C.; Willighagen, E. L. (2007), "Chemical
Markup, XML, and the World Wide Web. 7. CMLSpect, an
for Spectral Data",
J. Chem. Inf. Model. , 47 (6): 2015–2034, doi
:10.1021/ci600531a , PMID 17887743
* ^ JUMBO
* ^ Murray-Rust, P.; Rzepa, H. S. (2001), "Chemical Markup,
the World-Wide Web. 2. Information Objects and the CMLDOM", J. Chem.
Inf. Comput. Sci. , 41 (5), doi :10.1021/ci000404a
* ^ CML home on Sourceforge
* ^ Willighagen, E.L. (2000). "Processing CML Conventions in Java".
Chemistry Preprint Server.
* ^ Willighagen, E.L. (2001). "Processing CML Conventions in Java".
Internet Journal of Chemistry. 4.
* Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. (1997), "The
Internet as a Chemical Information Tool",
Chem. Soc. Rev. , 26 (1):
1–10, doi :10.1039/CS9972600001
* Murray-Rust, P.; Rzepa, H. S.; Wright, M. (2001), "Development of
Chemical Markup Language (CML) as a System for Handling Complex
New J. Chem. : 618–634