Chemical Markup Language

cml
Filename extension	.cml
Internet media type	chemical/x-cml
Type of format	chemical file format

Chemical Markup Language (ChemML or CML) is an approach to managing molecular information using tools such as XML and Java.^[1] It was the first domain specific implementation based strictly on XML, first based on a DTD^[2] and later on an XML Schema,^[3] 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 documents.^[4]

CML is capable of supporting a wide range of chemical concepts including:

molecules
reactions^[5]
spectra and analytical data^[6]
computational chemistry
chemical crystallography and materials

Details of CML and points currently under discussion are now posted on the CML Blog.

^ Murray-Rust, Peter; Rzepa, Henry S (2011). "CML: Evolution and design". Journal of Cheminformatics. 3 (1): 44. doi:10.1186/1758-2946-3-44. PMC 3205047. PMID 21999549.
^ 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, CiteSeerX 10.1.1.40.8275, doi:10.1021/ci990052b
^ Murray-Rust, P.; Rzepa, H. S. (2003), "Chemical Markup, XML and the World Wide Web. 4. CML Schema", J. Chem. Inf. Comput. Sci., 43 (3): 757–772, doi:10.1021/ci0256541, PMID 12767134
^ 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, PMID 11604013
^ Holliday, G. L.; Murray-Rust, P.; Rzepa, H. S. (2006), "Chemical Markup, 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, PMID 16426051
^ 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 XML Vocabulary for Spectral Data", J. Chem. Inf. Model., 47 (6): 2015–2034, doi:10.1021/ci600531a, PMID 17887743

[1] Murray-Rust, Peter; Rzepa, Henry S (2011). "CML: Evolution and design". Journal of Cheminformatics. 3 (1): 44. doi:10.1186/1758-2946-3-44. PMC 3205047. PMID 21999549.

[2] 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, CiteSeerX 10.1.1.40.8275, doi:10.1021/ci990052b

[3] Murray-Rust, P.; Rzepa, H. S. (2003), "Chemical Markup, XML and the World Wide Web. 4. CML Schema", J. Chem. Inf. Comput. Sci., 43 (3): 757–772, doi:10.1021/ci0256541, PMID 12767134

[4] 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, PMID 11604013

[5] Holliday, G. L.; Murray-Rust, P.; Rzepa, H. S. (2006), "Chemical Markup, 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, PMID 16426051

[6] 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 XML Vocabulary for Spectral Data", J. Chem. Inf. Model., 47 (6): 2015–2034, doi:10.1021/ci600531a, PMID 17887743

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