The application of chemical Multipurpose Internet Mail Extensions (chemical MIME) Internet standards to electronic mail and World Wide Web information exchange

Journal of Chemical Information and Computer Sciences

Volumn 38, Issue 6, 1998, Pages 976-982

  Rzepa, Henry S ^a   Murray Rust, Peter ^b   Whitaker, Benjamin J ^c  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000532520     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9803233     Document Type: Article

References (30)

1. Rzepa, H. S.; Murray-Rust, P.; and Whitaker, B. J. Chem. Soc. Rev. 1997, 1-10.
2. Borenstein, N.; Freed. N. "MIME (Multipurpose Internet Mail Extensions) Part One: Mechanisms for Specifying and Describing the Format of Internet Message Bodies"; Internet RFC 1521, Bellcore, Innosoft, September 1993.
3. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
4. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
5. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
6. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
7. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
8. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
9. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
10. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
11. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
12. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
13. Rzepa, H. S.; Whitaker, B. J.; Winter, M. J. J. Chem. Soc., Chem. Commun. 1994, 1907; Rzepa, H. S. Compur. Networks and ISDN Systems, 1994, 27, 317-318; Rzepa, H. S. Chem. Design Auto. News 1994, 9, 1; Rzepa, H. S. In The Internet: A Guide for Chemists; Bachrach, S., Ed.; American Chemical Society: Washington, D.C., 1995; Winter, M. J.; Rzepa, H. S.; Whitaker, B. J.; Chem. Br. 1995, 685; Davies, A. N. Spectrosc. Eur. 1996, 8, 42; Rzepa, H. S. Sci. Progress 1996, 79, 97; Whitaker, B. J.; Rzepa, H. S. Proc. Int. Chem. Inf. Conf. Collier, H., Ed.; 1995, 62-71; Rzepa, H. S.; Casher, O.; Whitaker, B J. Proc. Int. Chem. Inf. Conf. Collier. H., Ed.; 1996, 141-148; Rzepa, H. S.; Locke, W.; Murray-Rust, P.; Whitaker, B. J. In Perspect. Protein Eng. '96. Geisow, M. J., Ed.; 1996, Paper no. 19; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Chem. Intl. 1997, 19, 17.
14. A description of the definitive list will be published elsewhere; Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. Pure Appl. Chem., in preparation. The latest information is available on-line at http:// www.ch.ic.ac.uk/chemime/.
15. Rzepa, H. S. "Internet-based Computational Chemistry Tools", In Encyclopaedia of Computational Chemistry; Wiley: New York, in press.
16. An example of the use of chemical MIME to integrate a variety of chemical data types into the body of an electronic journal is the CLIC Electronic Journal Project; James, D.; Whitaker, B. J.; Hildyard, C.; Rzepa, H. S.; Casher, O.; Goodman, J. M.; Riddick, D.; Murray-Rust, P.;, New. Rev. Information Networking 1996, 61. For the project itself, see http://www.rsc.org/is/journals/current/chemcomm/cccenha.htm or the original site at http://chemcomm.clic.ac.uk/. For details of how a "chemically enhanced" article was prepared, see Casher, O.; Rzepa, H. S. In Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3. Rzepa, H. S., Leach,C., Eds.; Royal Society of Chemistry, 1998; ISBN (CD-ROM) 0-85404-889-8.
17. An example of the use of chemical MIME to integrate a variety of chemical data types into the body of an electronic journal is the CLIC Electronic Journal Project; James, D.; Whitaker, B. J.; Hildyard, C.; Rzepa, H. S.; Casher, O.; Goodman, J. M.; Riddick, D.; Murray-Rust, P.;, New. Rev. Information Networking 1996, 61. For the project itself, see http://www.rsc.org/is/journals/current/chemcomm/cccenha.htm or the original site at http://chemcomm.clic.ac.uk/. For details of how a "chemically enhanced" article was prepared, see Casher, O.; Rzepa, H. S. In Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3. Rzepa, H. S., Leach,C., Eds.; Royal Society of Chemistry, 1998; ISBN (CD-ROM) 0-85404-889-8.
18. For examples of the application of chemical MIME to electronic conferencing, see ECTOC-1 Leach, C., Rzepa, H. S., Eds.; Royal Society of Chemistry, 1996. Also ECHET96, 1997; ECTOC-3, 1998, and ECHET98, 1998. The conferences are on-line at http://www.ch.ic.ac.uk/ectoc/.
19. Maffett, T.; van Vliet, B. MDL Information Systems, 1996. For further details of Chime, see http://www.mdli.com/chemscape/chime/. This plug-in derives from the Rasmol program written by R. Sayle and applied within the chemical MIME project as described in Casher, O.; Chandramohan, G.; Hargreaves, M.; Leach, C.; Murray-Rust, P.; Sayle, R.; Rzepa, H. S.; Whitaker, B. J. J. Chem. Soc., Perkin Trans 2. 1995, 7.
20. Maffett, T.; van Vliet, B. MDL Information Systems, 1996. For further details of Chime, see http://www.mdli.com/chemscape/chime/. This plug-in derives from the Rasmol program written by R. Sayle and applied within the chemical MIME project as described in Casher, O.; Chandramohan, G.; Hargreaves, M.; Leach, C.; Murray-Rust, P.; Sayle, R.; Rzepa, H. S.; Whitaker, B. J. J. Chem. Soc., Perkin Trans 2. 1995, 7.
21. A simple test molecule is available at http://www.ch.ic.ac.uk/rzepa/ jcics/molecule.pdb. A site for testing an extended set of chemical MIME types is available at http://www-dsed.llnl.gov/documents/tests/ chem.html.
22. Rzepa, H. S., available as http://www.ch.ic.ac.uk/rzepa/jcics/ chemical10.hqx.
23. Pilling, M. J.; Saunders, S.; Jenkin, M.; Derwent, D. "Tropospheric Chemistry"; http://www.chem.leeds.ac.uk/Atmospheric/MCM/main.html.
24. For details of all W3C (World Wide Web Consortium) recommendations, proposed recommendations, working drafts and notes, see http: //www.w3.org/TR/.
25. Murray-Rust, P.;, "Chemical Markup Language, A simple introduction to structured documents" In XML, Principles, Tools and Techniques; Connolly, D., Ed.; O'Reilly: 1997; pp 135-149.
26. For specifications see Bourne, P. E.; Berman, H. M.; McMahon, B.; Watenpaugh, K. D.; Westbrook, J.; Fitzgerald, P. M. D. Methods Enzymol. 1997, 277, 571-590. See also http://www.iucr.org and http: //www.iucr.org/cif/mm/index.html.
27. Murray-Rust, P.; West, L. ASLIB Managing Information, 1997, 4, 36-39. See also http://www.vhg.org.uk/.
28. Murray-Rust, P.; In Proc. E. Conf. Trends in Organomet. Chem.: ECTOC-3; Rzepa, H. S., Leach, C., Eds.; Royal Society of Chemistry, 1998. ISBN (CD-ROM) 0-85404-889-8. A fully working version of JUMBO is included on this CD-ROM. See also ref 13, pp 197-207.
29. The CML project was first described in Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstracts of Papers, Am. Chem. Soc. 1995, 210, pp 40-COMP (http://www.ch.ic.ac.uk/cml/) and in Murray-Rust, P.; Rzepa, H. S. Abstracts of Papers, Am. Chem. Soc. 1997, 214, pp 23-COMP. Details of CML itself are available in refs 13 and 16. Further details will be published in a forthcoming paper.
30. The CML project was first described in Murray-Rust, P.; Leach, C.; Rzepa, H. S. Abstracts of Papers, Am. Chem. Soc. 1995, 210, pp 40-COMP (http://www.ch.ic.ac.uk/cml/) and in Murray-Rust, P.; Rzepa, H. S. Abstracts of Papers, Am. Chem. Soc. 1997, 214, pp 23-COMP. Details of CML itself are available in refs 13 and 16. Further details will be published in a forthcoming paper.