Chemical Markup Language - publications

This page lists CML-related publications by Peter Murray-Rust/Henry Rzepa and others. Publications are divided into two categories - CML technology and CML-supported/CML-enabled science - and listed in reverse chronological order (newest first).

CML technology

  1. "CMLLite: a design philosophy for CML", Joe Townsend & Peter Murray-Rust, J. Cheminform., 3:39 (2011) (DOI: 10.1186/1758-2946-3-39)
  2. "The semantics of Chemical Markup Language (CML): dictionaries and conventions", Peter Murray-Rust, Joe Townsend, Sam Adams, Weerapong Phadungsukanan & Jens Thomas, J. Cheminform., 3:43 (2011) (DOI: 10.1186/1758-2946-3-43)
  3. "CML: Evolution and Design", Peter Murray-Rust & Henry S. Rzepa, J. Cheminform., 3:44 (2011) (DOI: 10.1186/1758-2946-3-44)
  4. "Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language", Nico Adams, Jerry Winter, Peter Murray-Rust & Henry Rzepa, J. Chem. Inf. Model., 48(11), 2118-2128 (2008) (DOI: 10.1021/ci8002123)
  5. "XML and Its Application in Chemistry", Peter Murray-Rust & Henry S. Rzepa, chapter 16 in "Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes" (ed J. Gasteiger), pub. Wiley-VCH Verlag GmbH, Weinheim, Germany (2008) (DOI: 10.1002/9783527618279.ch16)
  6. "Chemical markup, XML, and the world wide web. 7. CMLSpect, an XML vocabulary for spectral data", Stefan Kuhn, Tobias Helmus, Robert Lancashire, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck & Egon Willighagen, J. Chem. Inf. Model., 47(6), 2015-2034 (2007) (DOI: 10.1021/ci600531a)
  7. "Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions", Gemma Holliday, Peter Murray-Rust & Henry Rzepa, J. Chem. Inf. Model., 46(1), 145-157 (2006) (DOI: 10.1021/ci0502698)
  8. "XML, Chemical Markup Language (CML) and the Datument", Peter Murray-Rust & Henry S. Rzepa, chapter 8 in "The ACS Style Guide: Effective Communication of Scientific Information (3rd edition)", (eds. Anne M. Coghill, Lorrin R. Garson; ISBN10: 0841239991) (2006)
  9. "CMLSnap: Animated reaction mechanisms", Gemma Holliday, John Mitchell & Peter Murray-Rust, Internet J. Chem., 7(4), Article Number: 4 (2004)
  10. "Chemical Markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators", Peter Murray-Rust, Henry Rzepa, Mark Williamson & Egon Willighagen, J. Chem. Inf. Comput. Sci., 44(2), 462-469 (2004) (DOI: 10.1021/ci034244p)
  11. "Chemical Markup, XML, and the World Wide Web. 4. CML Schema", Peter Murray-Rust & Henry Rzepa, J. Chem. Inf. Comput. Sci., 43(3), 757-772 (2003) (DOI: 10.1021/ci0256541)
  12. "XML for scientific publishing", Peter Murray-Rust & Henry S. Rzepa, OCLC Systems & Services, 19(4), 162-169 (2003) (DOI: 10.1108/10650750310698784)
  13. "STMML. A markup language for scientific, technical and medical publishing", Peter Murray-Rust & Henry Rzepa, Data Science J., 1, 128-192 (2002) (DOI: 10.2481/dsj.1.128)
  14. "Scientific publications in XML - towards a global knowledge base", Peter Murray-Rust & Henry S. Rzepa, Data Science J., 1, 84-98 (2002) (DOI: 10.2481/dsj.1.84)
  15. "Markup Languages - How to structure chemistry related documents", Peter Murray-Rust & Henry S. Rzepa, Chemistry Intl., 24(4), 9-13 (2002)
  16. "Chemical markup, XML, and the World-Wide Web. 3. Toward a signed semantic chemical web of trust", Giorgios Gkoutos, Peter Murray-Rust, Henry Rzepa & Michael Wright, J. Chem. Inf. Comput. Sci., 41(5), 1124-1130 (2001) (DOI: 10.1021/ci000406v)
  17. "Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM", Peter Murray-Rust & Henry Rzepa, J. Chem. Inf. Comput. Sci., 41(5), 1113-1123 (2001) (DOI: 10.1021/ci000404a)
  18. "Development of chemical markup language (CML) as a system for handling complex chemical content", Peter Murray-Rust, Henry Rzepa & Michael Wright, New J. Chem., 25(4), 618-634 (2001) (DOI: 10.1039/b008780g)
  19. "A resource for transforming HTML and molfile documents to XML compliant form", Giorgios Gkoutos, P. Kenway, Peter Murray-Rust, Henry Rzepa & Michael Wright, Internet J. Chem., 4(5), Article Number: 5
  20. "A universal approach to web-based chemistry using XML and CML", Peter Murray-Rust, Henry Rzepa, Michael Wright & Stephen Zara, Chem. Commun., 16, 1471-1472 (2000) (DOI: 10.1039/B002483J)
  21. "Chemical markup, XML, and the Worldwide Web. 1. Basic principles", Peter Murray-Rust & Henry Rzepa, J. Chem. Inf. Comput. Sci., 39(6), 928-942 (1999) (DOI: 10.1021/ci990052b)
  22. "The globalization of crystallographic knowledge", Peter Murray-Rust, Acta Cryst., D54(6, No. 1), 1065-1070 (1998) (DOI: 10.1107/S0907444998009366)
  23. "Chemical Markup Language", Peter Murray-Rust in "Electronic communication technologies: techniques and technologies for the 21st century", (ed M. Mitchard, Interpharm Press, Buffalo Grove, Ill. ISBN: 1574910698) (1998)
  24. "JUMBO: An Object-based XML Browser", Peter Murray-Rust, World Wide Web Journal, 2(4), 197-206 (1997)
  25. "Chemical Markup Language: A Simple Introduction to Structured Documents", Peter Murray-Rust, World Wide Web Journal, 2(4), 135-147 (1997)
  26. "Hyperactive molecules and the World-Wide-Web information system", Omer Casher, Gudge K. Chandramohan, Martin J. Hargreaves, Christopher Leach, Peter Murray-Rust, Henry S. Rzepa, Roger Sayle & Benjamin J. Whitaker, J. Chem. Soc., Perkin Trans. 2, 1, 7-11 (1995) (DOI: 10.1039/P29950000007)

CML-supported/-enabled science

  1. "Visions of a Semantic Molecular Future" thematic issue in Journal of Cheminformatics>
  2. "First-Principles Thermochemistry for Gas Phase Species in an Industrial Rutile Chlorinator", Raphael Shirley, Weerapong Phadungsukanan, Markus Kraft, Jim Downing, Nick Day & Peter Murray-Rust, J. Phys. Chem. A, 114(43), 11825-11832 (2010) (DOI: 10.1021/jp106795p)
  3. "Engineering Polymer Informatics: Towards the Computer-Aided Design of Polymers", Nico Adams & Peter Murray-Rust, Macromol. Rapid Commun., 29(8), 615-632 (2008) DOI: 10.1002/marc.200700832)
  4. "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms", Gemma Holliday, Daniel Almonacid, Gail Bartlett, Noel O'Boyle, James Torrance, Peter Murray-Rust, John Mitchell & Janet Thornton, Nucleic Acids Research, 35(SI), D515-D520 (2007) (DOI: 10.1093/nar/gkl774)
  5. "Usable grid infrastructures: practical experiences from the eMinerals project", M.T. Dove, A.M. Walker, T.O.H. White, R.P. Bruin, K.F. Austen, I. Frame, G.-T. Chiang, Peter Murray-Rust, R.P. Tyer, P.A. Couch, K. Kleese van Dam, S.C. Parker, A. Marmier & C. Arrouvel, Proceedings of the UK e-Science All Hands Meeting 2007, 48-55
  6. "Application and uses of CML within the eMinerals project", Toby White, Peter Murray-Rust, Phil Couch, Rik Tyer, Richard Bruin, Ilian Todorov, Dan Wilson, Martin Dove, Kat Austen & Steve Parker, Proceedings of the UK e-Science All Hands Meeting 2006, 606-613
  7. "Blue Obelisk - Interoperability in chemical informatics", Rajarshi Guha, Michael Howard, Geoffrey Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Jörg Wegner & Egon Willighagen, J. Chem. Inf. Model., 46(3), 991-998 (2006) (DOI: 10.1021/ci050400b
  8. "MACiE: a database of enzyme reaction mechanisms", Gemma Holliday, Gail Bartlett, Daniel Almonacid, Noel O'Boyle, Peter Murray-Rust, Janet Thornton & John Mitchell, Bioinformatics, 21(23), 4315-4316 (2005) (DOI: 10.1093/bioinformatics/bti693
  9. "CML tools and information flow in atomic scale simulations", J. Wakelin, Peter Murray-Rust, Simon Tyrrell, Yong Zhang, Henry Rzepa & A. García, Mol. Simulation, 31(5), 315-322 (2005) (DOI:10.1080/08927020500065850
  10. "The use of XML and CML in Computational Chemistry and Physics Programs", A. García, Peter Murray-Rust, J. Wakelin, Proceedings of the UK e-Science All Hands Meeting 2004, 1111-1114

The publications listed above are a selection from the full listings for Peter Murray-Rust and Henry Rzepa.