Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles

Journal of Chemical Information and Computer Sciences

Volumn 39, Issue 6, 1999, Pages 928-942

  Murray Rust, Peter ^b   Rzepa, Henry S ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000554921     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci990052b     Document Type: Article

References (25)

1. The CML project was first described in: Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstr. Pap.-Am. Chem. Soc. 1995, 210, 40-COMP. Murray-Rust, P.; Rzepa, H. S. Abstr. Pap. Am. Chem. Soc. 1997, 214, 23-COMP. Preliminary specifications, software components, and examples were published on CD-ROM in: Proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96); Rzepa, H. S., Snyder, J., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1997; ISBN 0-85404-894-4. Also: Proceedings of the Electronic Conference on Trends in Organometallic Chemistry (ECTOC3); Rzepa, H. S., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1998; ISBN 0-85404-889- 8.
2. The CML project was first described in: Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstr. Pap.-Am. Chem. Soc. 1995, 210, 40-COMP. Murray-Rust, P.; Rzepa, H. S. Abstr. Pap. Am. Chem. Soc. 1997, 214, 23-COMP. Preliminary specifications, software components, and examples were published on CD-ROM in: Proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96); Rzepa, H. S., Snyder, J., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1997; ISBN 0-85404-894-4. Also: Proceedings of the Electronic Conference on Trends in Organometallic Chemistry (ECTOC3); Rzepa, H. S., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1998; ISBN 0-85404-889- 8.
3. The CML project was first described in: Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstr. Pap.-Am. Chem. Soc. 1995, 210, 40-COMP. Murray-Rust, P.; Rzepa, H. S. Abstr. Pap. Am. Chem. Soc. 1997, 214, 23-COMP. Preliminary specifications, software components, and examples were published on CD-ROM in: Proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96); Rzepa, H. S., Snyder, J., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1997; ISBN 0-85404-894-4. Also: Proceedings of the Electronic Conference on Trends in Organometallic Chemistry (ECTOC3); Rzepa, H. S., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1998; ISBN 0-85404-889- 8.
4. The CML project was first described in: Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstr. Pap.-Am. Chem. Soc. 1995, 210, 40-COMP. Murray-Rust, P.; Rzepa, H. S. Abstr. Pap. Am. Chem. Soc. 1997, 214, 23-COMP. Preliminary specifications, software components, and examples were published on CD-ROM in: Proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96); Rzepa, H. S., Snyder, J., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1997; ISBN 0-85404-894-4. Also: Proceedings of the Electronic Conference on Trends in Organometallic Chemistry (ECTOC3); Rzepa, H. S., Leach, C., Eds.; The Royal Society of Chemistry: Cambridge, U.K., 1998; ISBN 0-85404-889-8.
5. This is more fully described in the XML1.0 Recommendation; http:// www.w3.org/xml/ and in particular http://www.w3.org/TR/xmlschemal/ and http://www.w3.org/TR/xmlschema-2/. See also: Graham, I., Quin, L. 1.0, XML Specification Guide; Wiley: New York, 1999; ISBN 0471327530.
6. Murray-Rust, P.; Rzepa, H. S.; Whittaker, B. J. Chem. Soc. Rev. 1997, 27, 1-10.
7. Weibel, S. Bull. Am. Soc. Inf. Sci. 1997, 24, 9-11. A model for medical metadata has been proposed; Malet, G.; Munoz, F.; Appleyard, R.; Hersh, W. J. Am. Med. Inf. Assoc. 1999, 6, 163-172. For metadata in chemistry, see: Gkoutos, G. V.; Murray-Rust, P.; Turner, A. N.; Rzepa, H. S. To be submitted for publication.
8. Weibel, S. Bull. Am. Soc. Inf. Sci. 1997, 24, 9-11. A model for medical metadata has been proposed; Malet, G.; Munoz, F.; Appleyard, R.; Hersh, W. J. Am. Med. Inf. Assoc. 1999, 6, 163-172. For metadata in chemistry, see: Gkoutos, G. V.; Murray-Rust, P.; Turner, A. N.; Rzepa, H. S. To be submitted for publication.
9. Weibel, S. Bull. Am. Soc. Inf. Sci. 1997, 24, 9-11. A model for medical metadata has been proposed; Malet, G.; Munoz, F.; Appleyard, R.; Hersh, W. J. Am. Med. Inf. Assoc. 1999, 6, 163-172. For metadata in chemistry, see: Gkoutos, G. V.; Murray-Rust, P.; Turner, A. N.; Rzepa, H. S. To be submitted for publication.
10. Hall, S. R.; Allen, F. H.; Brown, I. D. Acta Crystallogr. 1991, A47, 655-685.
11. See e.g.: Bryan, M. An Author's Guide to the Standard Generalized Markup Language; Addison-Wesley: Reading, MA, 1988. Goldfarb, C. F.; Runinsky, Y. The SGML Handbook; Clarendon Press: Oxford, U.K., 1990. Goldfarb, C. F.; Prescod, P. The XML Handbook; Prentice Hall: Englewood Cliffs, NJ, 1998.
12. See e.g.: Bryan, M. An Author's Guide to the Standard Generalized Markup Language; Addison-Wesley: Reading, MA, 1988. Goldfarb, C. F.; Runinsky, Y. The SGML Handbook; Clarendon Press: Oxford, U.K., 1990. Goldfarb, C. F.; Prescod, P. The XML Handbook; Prentice Hall: Englewood Cliffs, NJ, 1998.
13. See e.g.: Bryan, M. An Author's Guide to the Standard Generalized Markup Language; Addison-Wesley: Reading, MA, 1988. Goldfarb, C. F.; Runinsky, Y. The SGML Handbook; Clarendon Press: Oxford, U.K., 1990. Goldfarb, C. F.; Prescod, P. The XML Handbook; Prentice Hall: Englewood Cliffs, NJ, 1998.
14. Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. J. Chem. Inf. Comput. Sci. 1998, 38, 976-982.
15. For further details of Unicode, see: http://www.unicode.org/. The Unicode Standard. Version 2.0; NISP Press: 1996.
16. See for example: http://www.iucr.ac.uk/.
17. Pauling, L. The nature of the chemical bond and the structure of molecules and crystals: An introduction to modern structural, 2nd ed.; Cornell University Press: Ithaca, NY, 1942.
18. Bernal, J. D. Science in History, 3rd ed.; C. A. Watts: London, 1965.
19. Murray-Rust, P. http://www.xml-cml.org/.
20. These are elaborated in more detail at: http://www.w3.org/TR/REC-xml.
21. This will be explored in more depth in part 2 of this series.
22. Murray-Rust, P. Unpublished work.
23. Some early versions of CML used only these elements (see also ref 1).
24. For readers familiar with earlier versions of CML, note that some built-in values are obsolete since they do not describe the essential identity of the components. The current values are limited to those for which processing software needs to be provided.
25. These examples, together with the CML DTD shown in Chart 1, are included in Supporting Information with this Journal and are also available at: http://www.xml-cml.org/.