Difference between revisions of "Chemical Markup Language"
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| − | + | {{Infobox file format | |
| + | | name = cml | ||
| + | | extension = <tt>.cml</tt> | ||
| + | | mime = | ||
| + | | owner = | ||
| + | | creatorcode = | ||
| + | | genre = [[chemical file format]] | ||
| + | | container for = | ||
| + | | contained by = | ||
| + | | extended from = | ||
| + | | extended to = | ||
| + | }} | ||
| − | '''CML''' ('''C'''hemical '''M'''arkup '''L'''anguage) is | + | '''CML''' ('''C'''hemical '''M'''arkup '''L'''anguage) is an approach to managing [[molecular]] information using tools such as [[XML]] and [[Java platform|Java]]. It was the first domain specific implementation based strictly on [[XML]], 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 | + | 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. |
CML is capable of supporting a wide range of chemical concepts including: | CML is capable of supporting a wide range of chemical concepts including: | ||
| Line 12: | Line 23: | ||
* chemical crystallography and materials | * chemical crystallography and materials | ||
| − | Details of CML are now | + | Details of CML and points currently under discussion are now posted on the CML Blog. |
== Versioning == | == Versioning == | ||
| − | The latest versions of the schema are available at Sourceforge | + | The latest versions of the schema are available at Sourceforge. The latest frozen schema is CML2.4. A number of constructs in CML1 were DTD-based and are now deprecated so users should consider using CML v2. |
== Tools == | == Tools == | ||
| − | JUMBO is an extensive Java library supporting all elements in the schema | + | 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 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]]. See [[Blue Obelisk]]. |
==See also== | ==See also== | ||
| Line 25: | Line 36: | ||
* Software importing and exporting a valid CML format | * Software importing and exporting a valid CML format | ||
**[[Bioclipse]] | **[[Bioclipse]] | ||
| − | **[[CDK]] | + | **[[Chemistry Development Kit|CDK]] |
**[[JOELib]] | **[[JOELib]] | ||
**[[OpenBabel]] | **[[OpenBabel]] | ||
| − | *[[Joint Committee on Atomic and Molecular Physical Data]] (another well | + | *[[Joint Committee on Atomic and Molecular Physical Data]] (another well-known standard, especially for spectroscopic data) |
| + | *[[Blue Obelisk]] community for Open Source chemical software | ||
==External links == | ==External links == | ||
| − | *[http://cml.sourceforge.net/ Chemical Markup Language (CML)] | + | *[http://cml.sourceforge.net/ 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://wwmm.ch.cam.ac.uk/blogs/cml/ CML Blog] | ||
*[http://xml-cml.org/ The original (old) site] | *[http://xml-cml.org/ The original (old) site] | ||
*[http://jmol.sourceforge.net/ The Jmol Browser's site] | *[http://jmol.sourceforge.net/ The Jmol Browser's site] | ||
| − | |||
| − | |||
| − | |||
| − | |||
== References == | == References == | ||
| + | {{reflist}} | ||
| + | {{No footnotes|date=July 2009}} | ||
# H. S. Rzepa, P. Murray-Rust and B. J. Whitaker ''The Internet as a Chemical Information Tool'' , Chem. Soc. Revs, '''1997''', 1-10. {{DOI|10.1039/CS9972600001}} | # H. S. Rzepa, P. Murray-Rust and B. J. Whitaker ''The Internet as a Chemical Information Tool'' , Chem. Soc. Revs, '''1997''', 1-10. {{DOI|10.1039/CS9972600001}} | ||
| − | # P. | + | # P. Murray—Rust and H. S. Rzepa, ''Chemical Markup, XML, and the World Wide Web. 1. Basic Principles'', J. Chem. Inf. Comput. Sci., '''1999''', ''39'', 928-942. {{DOI|10.1021/ci990052b}} |
| − | # P. | + | # E. L. Willighagen, ''Processing CML Conventions in Java'', Chemistry Preprint Server, '''2000'''. [http://www.sciencedirect.com/preprintarchive CPS Archives]; E. L. Willighagen, ''Processing CML Conventions in Java'', Internet Journal of Chemistry, '''2001''', ''4''. [http://www.ijc.com/abstracts/abstract4n4.html Abstract] |
| − | # G. V. Gkoutos and P. | + | # P. Murray—Rust and H. S. Rzepa, ''Chemical Markup, XML and the World—Wide Web. 2. Information Objects and the CMLDOM'', J. Chem. Inf. Comput. Sci., '''2001''', ''41''. {{DOI|10.1021/ci000404a}} |
| − | + | # G. V. Gkoutos and P. Murray—Rust and S. Rzepa and M. Wright, ''Chemical Markup, XML, and the World-Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust'', J. Chem. Inf. Comput. Sci., '''2001''', ''41'', 1124-1130. {{DOI|10.1021/ci000406v}} | |
# P. Murray-Rust, H. S. Rzepa and M. Wright, ''Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content'', New J. Chem., '''2001''', 618-634. | # P. Murray-Rust, H. S. Rzepa and M. Wright, ''Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content'', New J. Chem., '''2001''', 618-634. | ||
| − | # P. | + | # P. Murray—Rust and H. S. Rzepa, ''Chemical Markup, XML and the World—Wide Web. 4. CML Schema'', J. Chem. Inf. Comput. Sci. '''2003''', ''43'', 757-772. {{DOI|10.1021/ci0256541}} |
| − | # P. | + | # P. Murray—Rust and H. S. Rzepa and J. Williamson and E. L. Willighagen, ''Chemical Markup, XML and the World—Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators'', J. Chem. Inf. Comput. Sci., '''2004''', ''44'', 462-469. {{DOI|10.1021/ci034244p}} |
| − | #G. L. Holliday, P. Murray-Rust, H. S. Rzepa, ''Chemical Markup, XML and the | + | # G. L. Holliday, P. Murray-Rust, H. S. Rzepa, ''Chemical Markup, XML and the World Wide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions'', J. Chem. Inf. Mod., '''2006''', ''46'', 145-157. {{DOI|10.1021/ci0502698}} |
| + | # S. Kuhn, T. Helmus, R. J. Lancashire, P. Murray-Rust, H. S. Rzepa, C. Steinbeck, E. L. Willighagen , ''Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data'', J. Chem. Inf. Mod., '''2007''', ''47'', 2015 -2034. {{DOI|10.1021/ci600531a}} | ||
[[Category:Chemical information]] | [[Category:Chemical information]] | ||
| + | |||
| + | {{Imported from Wikipedia|name=Chemical Markup Language|id=304215699}} | ||
Latest revision as of 11:47, 31 July 2009
CML (Chemical Markup Language) 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, 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.
CML is capable of supporting a wide range of chemical concepts including:
- molecules
- reactions
- 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.
Versioning
The latest versions of the schema are available at Sourceforge. The latest frozen schema is CML2.4. A number of constructs in CML1 were DTD-based and are now deprecated so users should consider using CML v2.
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.[1] JUMBO has evolved into an extensive Java library supporting all elements in the schema.[2] Although JUMBO used to be a browser, the preferred approach is to use the Open Source tools Jmol and JChemPaint. See Blue Obelisk.
See also
- List 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
External links
- Chemical Markup Language (CML) This includes the CML Schema, links to tools, documentation, and source code
- Discussion list
- CML Blog
- The original (old) site
- The Jmol Browser's site
References
- H. S. Rzepa, P. Murray-Rust and B. J. Whitaker The Internet as a Chemical Information Tool , Chem. Soc. Revs, 1997, 1-10. DOI:10.1039/CS9972600001
- P. Murray—Rust and H. S. Rzepa, Chemical Markup, XML, and the World Wide Web. 1. Basic Principles, J. Chem. Inf. Comput. Sci., 1999, 39, 928-942. DOI:10.1021/ci990052b
- E. L. Willighagen, Processing CML Conventions in Java, Chemistry Preprint Server, 2000. CPS Archives; E. L. Willighagen, Processing CML Conventions in Java, Internet Journal of Chemistry, 2001, 4. Abstract
- P. Murray—Rust and H. S. Rzepa, Chemical Markup, XML and the World—Wide Web. 2. Information Objects and the CMLDOM, J. Chem. Inf. Comput. Sci., 2001, 41. DOI:10.1021/ci000404a
- G. V. Gkoutos and P. Murray—Rust and S. Rzepa and M. Wright, Chemical Markup, XML, and the World-Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust, J. Chem. Inf. Comput. Sci., 2001, 41, 1124-1130. DOI:10.1021/ci000406v
- P. Murray-Rust, H. S. Rzepa and M. Wright, Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content, New J. Chem., 2001, 618-634.
- P. Murray—Rust and H. S. Rzepa, Chemical Markup, XML and the World—Wide Web. 4. CML Schema, J. Chem. Inf. Comput. Sci. 2003, 43, 757-772. DOI:10.1021/ci0256541
- P. Murray—Rust and H. S. Rzepa and J. Williamson and E. L. Willighagen, Chemical Markup, XML and the World—Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators, J. Chem. Inf. Comput. Sci., 2004, 44, 462-469. DOI:10.1021/ci034244p
- G. L. Holliday, P. Murray-Rust, H. S. Rzepa, Chemical Markup, XML and the World Wide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions, J. Chem. Inf. Mod., 2006, 46, 145-157. DOI:10.1021/ci0502698
- S. Kuhn, T. Helmus, R. J. Lancashire, P. Murray-Rust, H. S. Rzepa, C. Steinbeck, E. L. Willighagen , Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data, J. Chem. Inf. Mod., 2007, 47, 2015 -2034. DOI:10.1021/ci600531a
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This page was originally imported from Wikipedia, specifically this version of the article "Chemical Markup Language". Please see the history page on Wikipedia for the original authors. This WikiChem article may have been modified since it was imported. It is licensed under the Creative Commons Attribution–Share Alike 3.0 Unported license. |
