Editing Chemical Markup Language (section)

{{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.