Editing Chemical Markup Language

{{short description|Markup language and file format}}
{{Infobox file format
| name = cml
| extension = .cml
| mime = 
| owner = 
| creatorcode = 
| genre = [[chemical file format]]
| container for = 
| contained by = 
| extended from = 
| extended to = 
}}

'''Chemical Markup Language''' ('''ChemML''' or '''CML''') is an approach to managing [[molecular]] information using tools such as [[XML]] and [[Java platform|Java]].<ref>{{cite journal|last1=Murray-Rust|first1=Peter|last2=Rzepa|first2=Henry S|title=CML: Evolution and design|journal=[[Journal of Cheminformatics]]|date=2011|volume=3|issue=1|pages=44|doi=10.1186/1758-2946-3-44|pmid=21999549|pmc=3205047 |doi-access=free }}</ref> It was the first domain specific implementation based strictly on [[XML]], first based on a [[Document Type Definition|DTD]]<ref>{{Citation
 |first1= P.
 |last1= Murray-Rust
 |first2= H. S.
 |last2= Rzepa
 |title= Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles
 |journal= [[J. Chem. Inf. Comput. Sci.]]
 |year= 1999
 |volume= 39
 |issue= 6
 |pages= 928&ndash;942
 |issn=
 |doi= 10.1021/ci990052b|citeseerx= 10.1.1.40.8275
 }}</ref> and later on an [[XML Schema (W3C)|XML Schema]],<ref>{{Citation
 |first1= P.
 |last1= Murray-Rust
 |first2= H. S.
 |last2= Rzepa
 |title= Chemical Markup, XML and the World Wide Web. 4. CML Schema
 |journal= [[J. Chem. Inf. Comput. Sci.]]
 |year= 2003
 |volume= 43
 |issue= 3
 |pages= 757&ndash;772
 |issn=
 |doi= 10.1021/ci0256541|pmid= 12767134
 }}</ref> the most robust and widely used system for precise information management in many areas. It has been developed over more than a decade by [[Peter Murray-Rust|Murray-Rust]], [[Henry Rzepa|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 [[Rich Site Summary|RSS]] documents.<ref>{{Citation
 |first1= G. V.
 |last1= Gkoutos
 |first2= P.
 |last2= Murray-Rust
 |first3= S.
 |last3= Rzepa
 |first4= M.
 |last4= Wright
 |title= Chemical Markup, XML, and the World-Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust
 |journal= [[J. Chem. Inf. Comput. Sci.]]
 |year= 2001
 |volume= 41
 |issue= 5
 |pages= 1124&ndash;1130
 |issn=
 |doi= 10.1021/ci000406v|pmid= 11604013
 }}</ref>

CML is capable of supporting a wide range of chemical concepts including:
* molecules
* reactions<ref>{{Citation
 |first1= G. L.
 |last1= Holliday
 |first2= P.
 |last2= Murray-Rust
 |first3= H. S.
 |last3= Rzepa
 |title= Chemical Markup, XML and the World Wide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions
 |journal= [[J. Chem. Inf. Model.]]
 |year= 2006
 |volume= 46
 |issue= 1
 |pages= 145&ndash;157
 |issn=
 |doi= 10.1021/ci0502698|pmid= 16426051
 }}</ref>
* spectra and analytical data<ref>{{Citation
 |first1= S.
 |last1= Kuhn
 |first2= T.
 |last2= Helmus
 |first3= R. J.
 |last3= Lancashire
 |first4= P.
 |last4= Murray-Rust
 |first5= H. S.
 |last5= Rzepa
 |first6= C.
 |last6= Steinbeck
 |first7= E. L.
 |last7= Willighagen
 |title= Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data
 |journal= [[J. Chem. Inf. Model.]]
 |year= 2007
 |volume= 47
 |issue= 6
 |pages= 2015&ndash;2034
 |issn=
 |doi=10.1021/ci600531a
 |pmid=17887743}}</ref>
* [[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]]. 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.<ref>[http://www.ch.ic.ac.uk/omf/cml/doc/jumbo/faq.html JUMBO]</ref> JUMBO has evolved into an extensive Java library, CMLDOM,<ref>{{Citation
 |first1= P.
 |last1= Murray-Rust
 |first2= H. S.
 |last2= Rzepa
 |title= Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM
 |journal= [[J. Chem. Inf. Comput. Sci.]]
 |year= 2001
 |volume= 41
 |issue= 5
 |issn=
 |doi= 10.1021/ci000404a
 |pages=1113–1123|pmid= 11604012
 }}</ref> supporting all elements in the schema.<ref>[http://sourceforge.net/projects/cml/ CML home on Sourceforge]</ref> Although JUMBO used to be a browser, the preferred approach is to use the Open Source tools [[Jmol]] and [[JChemPaint]], some of which use alternative CML libraries.<ref>{{cite journal|first1=E.L.|last1=Willighagen|title=Processing CML Conventions in Java|journal=Internet Journal of Chemistry|year=2001|volume=4|url=http://www.ijc.com/abstracts/abstract4n4.html|archive-url=https://web.archive.org/web/20010411081458/http://www.ijc.com/abstracts/abstract4n4.html|archive-date=2001-04-11}}</ref> See [[Blue Obelisk]].

==Software support==
Software importing and exporting a valid CML format
*[[Bioclipse]]
*[[Chemistry Development Kit|CDK]]
*[[JOELib]]
*[[OpenBabel]]
*[[Avogadro (software)|Avogadro]]
*[[XDrawChem]]
*[[OpenChrom]]

==See also==
*[[List of document markup languages]]
*[[Blue Obelisk]] community for Open Source chemical software
*[[Comparison of document markup languages]]
*[[JCAMP-DX]] (another well-known standard, especially for spectroscopic data)
*[[MathML]]

== References ==
{{Reflist|30em}}

== Further reading ==

*{{Citation
 |first1= H. S.
 |last1= Rzepa
 |first2= P.
 |last2= Murray-Rust
 |first3= B. J.
 |last3= Whitaker
 |title= The Internet as a Chemical Information Tool
 |journal= [[Chem. Soc. Rev.]]
 |year= 1997
 |volume= 26
 |issue= 1
 |pages= 1&ndash;10
 |doi= 10.1039/CS9972600001}}
*{{Citation
 |first1= P.
 |last1= Murray-Rust
 |first2= H. S.
 |last2= Rzepa
 |first3= M.
 |last3= Wright
 |title= Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content
 |journal= [[New J. Chem.]]
 |year= 2001
 |volume=25
 |issue=4
 |pages= 618&ndash;634
 |issn=
 |doi=10.1039/b008780g}}

==External links ==
*[http://www.xml-cml.org/documentation/index.html Chemical Markup Language (CML)] This includes the CML Schema, links to tools, documentation, and source code
*[http://cml.sourceforge.net/list/index.html Discussion list]
*[http://www.xml-cml.org/blog/ CML Blog]
*[http://xml-cml.org/ The original (old) site]

{{Document markup languages}}

[[Category:Markup languages]]
[[Category:Industry-specific XML-based standards]]
[[Category:Chemical file formats]]
[[Category:Cheminformatics]]
[[Category:Computational chemistry]]
[[Category:Computer-related introductions in 1999]]