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Wikipedia

Chemical Markup Language

December 15, 2023

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.

cml
Filename extension
.cml
Internet media typechemical/x-cml
Type of formatchemical file format

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:

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

Versioning edit

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 edit

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.[7] JUMBO has evolved into an extensive Java library, CMLDOM,[8] supporting all elements in the schema.[9] 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.[10] See Blue Obelisk.

Software support edit

Software importing and exporting a valid CML format

See also edit

References edit

  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
  7. ^ JUMBO
  8. ^ Murray-Rust, P.; Rzepa, H. S. (2001), "Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM", J. Chem. Inf. Comput. Sci., 41 (5): 1113–1123, doi:10.1021/ci000404a, PMID 11604012
  9. ^ CML home on Sourceforge
  10. ^ Willighagen, E.L. (2001). . Internet Journal of Chemistry. 4. Archived from the original on 2001-04-11.

Further reading edit

  • 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 Chemical Content", New J. Chem., 25 (4): 618–634, doi:10.1039/b008780g

External links edit

  • 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

December 15, 2023
chemical, markup, language, chemml, approach, managing, molecular, information, using, tools, such, java, first, domain, specific, implementation, based, strictly, first, based, later, schema, most, robust, widely, used, system, precise, information, managemen. 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 cmlFilename extension cmlInternet media typechemical x cmlType of formatchemical file formatChemical 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 materialsDetails of CML and points currently under discussion are now posted on the CML Blog Contents 1 Versioning 2 Tools 3 Software support 4 See also 5 References 6 Further reading 7 External linksVersioning editVersions 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 editJUMBO 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 7 JUMBO has evolved into an extensive Java library CMLDOM 8 supporting all elements in the schema 9 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 10 See Blue Obelisk Software support editSoftware importing and exporting a valid CML format Bioclipse CDK JOELib OpenBabel Avogadro XDrawChemSee also editList of document markup languages Comparison of document markup languages Joint Committee on Atomic and Molecular Physical Data another well known standard especially for spectroscopic data Blue Obelisk community for Open Source chemical software MathMLReferences edit 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 JUMBO Murray Rust P Rzepa H S 2001 Chemical Markup XML and the World Wide Web 2 Information Objects and the CMLDOM J Chem Inf Comput Sci 41 5 1113 1123 doi 10 1021 ci000404a PMID 11604012 CML home on Sourceforge Willighagen E L 2001 Processing CML Conventions in Java Internet Journal of Chemistry 4 Archived from the original on 2001 04 11 Further reading editRzepa 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 Chemical Content New J Chem 25 4 618 634 doi 10 1039 b008780gExternal links editChemical 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 Retrieved from https en wikipedia org w index php title Chemical Markup Language amp oldid 1188119890, wikipedia, wiki, book, books, library,

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