CML Peer Reviewed Publications and Reviews


  1. The Internet as a Chemical Information Tool, H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, Chem. Soc. Revs, 1997, 1-10. DOI: 10.1039/CS9972600001
  2. Chemical Markup Language, P. Murray-Rust World Wide Web Journal, 1997, pp 135-147 and "JUMBO, An Object-based XML Browser", ibid, 1997, pp 197-206. Published as chapters in "XML principles, Tools and Techniques", Ed. D. Connolly, 1997, O'Reilly.
  3. Internet-based Computational Chemistry Tools, H. S. Rzepa, in "Encyclopaedia of Computational Chemistry", Wiley, 1998, 1426.
  4. Chemical Markup Language, P. Murray-Rust, in "Electronic communication technologies. techniques and technologies for the 21st century", 1998, Ed M. Mitchard, Interpharm Press, Buffalo Grove, Ill. ISBN: 1574910698.
  5. Chemical markup Language and XML Part I. Basic principles, P. Murray-Rust and H. S. Rzepa, J. Chem. Inf. Comp. Sci., 1999, 39, 928. DOI: 10.1021/ci990052b
  6. A Universal approach to Web-based Chemistry using XML and CML, P. Murray-Rust, H. S. Rzepa, M. Wright and S. Zara, ChemComm, 2000, 1471-1472. See also supplemental information.
  7. Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content, Peter Murray-Rust, Henry S. Rzepa and Michael Wright, New J. Chem., 2001, 618-634. See also supplemental information.
  8. A Resource for Transforming HTML and Molfile Documents to XML Compliant Form, Georgios V. Gkoutos, Philip R. Kenway, Peter Murray-Rust, Henry S. Rzepa and Michael Wright, Internet J. Chem, 2001, article 5. See also supplemental information.
  9. Chemical Markup, XML and the World-Wide Web. Part II: Information Objects and the CMLDOM. P. Murray-Rust and H. S. Rzepa, J. Chem. Inf. Comp. Sci., 2001, 41, 1113. DOI: 10.1021/ci000404a
  10. Chemical Markup, XML and the World-Wide Web. Part III: Towards a signed semantic Chemical Web of Trust, G. Gkoutos, P. Murray-Rust, H. S. Rzepa and M. Wright, J. Chem. Inf. Comp. Sci., 2001, 41, 1124. DOI: 10.1021/ci000406v
  11. A New Publishing Paradigm: STM Articles as part of the Semantic Web, H. S. Rzepa and P. Murray-Rust, Learned Publishing, 2001, 14, 177.
  12. The Application of XML Languages for Integrating Molecular Resources, G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Internet J. Chemistry, 2001, article 13.
  13. Scientific publications in XML - towards a global knowledge base, P. Murray-Rust and H. S. Rzepa, Data Science, 2002, 1, 84-98.
  14. STMML. A Markup Language for Scientific, Technical and Medical Publishing, P. Murray-Rust and H. S. Rzepa, Data Science, 2002, 1, 1-65.
  15. P. Murray-Rust and H. S. Rzepa, "Markup Languages- How to structure chemistry related documents", Chemistry Intl., 2002, 24(4), 9-13.
  16. P. Murray-Rust, and H. S. Rzepa "Towards the Chemical Semantic Web", Proc. 2002 International Chemical Information Conference,, ed H. Collier. (Infonortics) 2002, pp 127-139.
  17. G. V. Gkoutos, H. S. Rzepa P. Murray-Rust, "Online Validation and Comparison of Molfile and CML Molecular Atom-Connection Descriptors", Internet J. Chem., 2003, article 1.
  18. P. Murray-Rust and H. S. Rzepa, chapter in "Chemoinformatics - From Data to Knowledge. Part 2. Advanced Topics.", ed. J. Gasteiger, 2003, in press.
  19. P. Murray-Rust and H. S. Rzepa, "Chemical Markup, XML and the Worldwide Web. Part 4. CML Schema", J. Chem. Inf. comp. Sci.,, 2003, 757 - 772. DOI: 10.1021/ci0256541
  20. P. Murray-Rust and H. S. Rzepa, "Towards the Chemical Semantic Web. An introduction to RSS ", Internet J. Chem., 2003, 6, article 4.
  21. P. Murray-Rust and H. S. Rzepa, "XML for scientific publishing", OCLC Systems and Services, 2003, 19, 162-169.
  22. P. Murray-Rust and H. S. Rzepa, "The Next Big Thing: From Hypermedia to Datuments", J. Digital Inf., 2004, 5, article 248, 2004-03-18.
  23. P. Murray-Rust, H. S. Rzepa, M. J. Williamson and E. L. Willighagen, "Chemical Markup, XML and the Worldwide Web. Part 5. Applications of Chemical Metadata in RSS Aggregators", J. Chem. Inf. Comp. Sci.,, 2004, 44, 462-469. See also supporting information and DOI: 10.1021/ci034244p
  24. P. Murray-Rust, H. S. Rzepa, S. M. Tyrrell and Y. Zhang, "Representation and use of Chemistry in the Global Electronic Age", Org. Biomol. Chem., 2004, 2, 3192 to 3203. DOI: 10.1039/B410732B
  25. P. Murray-Rust, H. S. Rzepa and S. Stein, "The INChI as an LSID for molecules in lifescience", W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
  26. P. Murray-Rust, H. S. Rzepa, "Towards a semantic web for chemistry in lifescience", W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
  27. P. Murray-Rust, H. S. Rzepa and Y. Zhang, "Googling for INChIs; A remarkable method of chemical searching", W3C Workshop on Semantic Web for Life Sciences, 27-28 October 2004, Cambridge, Massachusetts USA.
  28. J. Wakelin, P. Murray-Rust, S. Tyrrell, Y. Zhang, H.S. Rzepa, A Garcia, "CML Tools and Information Flow in Atomic Scale Simulations", Mol. Simulations, 2005, 31, 315-322. DOI: 10.1080/08927020500065850
  29. P. Murray-Rust, H. S. Rzepa, J. J. P. Stewart and Y. Zhang, "A global resource for computational chemistry", J. Mol. Mod., 2005, 11, DOI: 10.1007/s00894-005-0278-1
  30. Si. J. Coles, N. E. Day, P. Murray-Rust, H. S. Rzepa and Y. Zhang, "Enhancement of the Chemical Semantic Web through INChIfication", Org. Biomol. Chem., 2005, 3, 1832-1834. DOI: 10.1039/b502828k
  31. P. Murray-Rust, John B.O. Mitchell and H. S. Rzepa, "Chemistry in Bioinformatics", BMC Bioinformatics, 2005, 6:141, DOI:10.1186/1471-2105-6-141.
  32. P. Murray-Rust, John B.O. Mitchell and H. S. Rzepa, "Communication and re-use of chemical information in bioscience", BMC Bioinformatics, 2005, 6:180, DOI: 10.1186/1471-2105-6-180
  33. G. L. Holliday, P. Murray-Rust, H. S. Rzepa, "Chemical Markup, XML and the Worldwide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions", J. Chem. Inf. Mod., 2006, 46, 145-147. DOI: 10.1021/ci0502698
  34. P. Murray-Rust and H. S. Rzepa, "XML, Chemical Markup Language (CML) and the Datument", chapter 8 in: The ACS Style Guide, 3rd edition, 2006. ISBN10: 0841239991, ISBN13: 9780841239999
  35. R. Guha , M. T. Howard, G. R. Hutchison, P. Murray-Rust, H. S. Rzepa C. Steinbeck, J. Wegner, E. L. Willighagen, "The Blue Obelisk - Interoperability in Chemical Informatics", J. Chem. Inf. Mod., 2006, 46, 991-998. DOI: 10.1021/ci050400b
  36. S. Kuhn, P. Murray-Rust, R. John Lancashire, Henry S. Rzepa, T. Helmusk, E. L. Willighagen, C. Steinbeck, "Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data", 2007, J. Chem. Inf. Mod., in press.
A number of these articles have associated supplemental information which demonstrates the use of CML.
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