XyM Markup Language (XyMML) for Electronic Communication of Chemical Documents Containing Structural Formulas and Reaction Schemes

Journal of Chemical Information and Computer Sciences

Volumn 39, Issue 6, 1999, Pages 915-927

  Fujita, Shinsaku ^a  

^a KYOTO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0008944556     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci990029q     Document Type: Article

References (37)

1. ISO 8879-1996 (JIS X 4151-1992) Information processing, Text and office systems, Standard Generalized Markup Language (SGML).
2. van Hervijnen, E. Practical SGML; Kluwer Academic: Dordrecht, The Netherlands, 1990.
3. Bryan, M. SGML. An Author's Guide to the Standard Generalized Markup Language; Addison-Wesley: Reading, MA, 1988.
4. Itoh, T. Kagaku to Kogyo (Tokyo) 1993, 46, 66.
5. Knuth, D. E. The TeXbook; Addison-Wesley: Reading, MA, 1984.
6. Lamport, L. LaTeX. A Document Preparation System, 2nd ed.; Addison-Wesley: Reading, MA, 1994.
7. Garson, L. ACS' SGML Activities, http://www.oasis-open.org/cover/ garson0054.html, 1994.
8. ISO 12083-1994 (JIS X 0804-1996) Information and documentation, Electronic manuscript preparation and markup.
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10. Wiggins, G. Chemistry on the Internet: The Library on Your Computer. J. Chem. Inf. Comput. Sci. 1998, 38, 956-965.
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13. Extensible Markup Language (XML), http://www.w3.org/XML.
14. CSJ's home page, http://wwwsoc.nacsis.ac.jp/csj/index.html.
15. 24
16. Raggett, D. W3C Activity: Math, http://www.w3.org/pub/WWW/TR/ PR-math/.
17. Murray-Rust, P.; Rzepa, H. S.; Leach, C. CML-Chemical Markup Language. Presented as a Poster at the 210th ACS Meeting in Chicago, 1995; Abstract 40 (http://www.chi.ic.ac.uk/cml/).
18. Fujita, S. XyMTeX. A macro package for typesetting chemical structural formulas. On-line Manual for XyMTeX, Version 1.00; CTAN: ftp://ctan.tug.org/tex-archive/macros/latex/contrib/other/ xymtex/, 1993.
19. Fujita, S. Typesetting structural formulae with the text formatter TeX/ LaTeX. Comput. Chem. 1994, 18, 109-116.
20. Fujita, S. XyMTeX for drawing chemical structural formulas. TUG-boats 1995, 16, 80-88.
21. Fujita, S. XyMTeX. A macro package set for typesetting chemical structural formulas. On-line Manual for XyMTeX, Version 1.01; 1996. This can be obtained from the author's cite (see ref 37) and from the CD-ROM attached to ref 22.
22. Fujita, S. XyMTeX. Typesetting Chemical Structural Formulas; Addison-Wesley Japan: Tokyo, 1997.
23. Ogura, T.; Nishimoto, M.; Hatano, Y. Representation of Mathematical Formula, Chemical Formula and Structral Formula on the WWW Browser. In The 20th Symposium on Chemical Information and Computer Science, Kumamoto; Chemical Society of Japan: Tokyo, Japan, 1997; p 21IP15.
24. Fujita, S.; Tanaka, N. XyM Notation for Electronic Communication of Organic Chemical Structures. J. Chem. Inf. Comput. Sci. 1999, 39, 903-914.
25. Lafore, R. Data Structure and Algorithms in Java; Waite Group: 1998; Japanese Translation, Softbank: Tokyo, 1999.
26. Active X Whitepaper: http://www.microsoft.co.jp/internet/activex/ index.htm.
27. YM). The pronunciation of XyM is recommended to be "khým", in which the "kh" sound may be a Russian "kh" or more simply an English "k" and the symbol "y" is expected to be pronounced like a German "ü". Note that the word "chemistry" stems from an Arabian root "alchemy", which is, in turn, considered to come from Greek, χυμείᾱ.
28. Davis, C. H.; Rush, J. E. Information Retrieval and Documentation in Chemistry; Greenwood: Westport, CT, 1974.
29. Gould, E. S. Mechanism and Structure in Organic Chemistry; Henry Holt: New York, 1959; p 643.
30. Fujita, S. Synthesis and reactions of o-benzoquinone monosulfonimides. J. Org. Chem. 1983, 48, 177-183, and references cited therein.
31. The parsing of the XyMML should be done after the SGML declaration containing a line "QUANTITY SGMLREF TAGLVL 50" to expand the limit of the maximum number of opening tags, since the default value of TAGLVL (=24) is short in giving a sufficient result.
32. Fujita, S. Canonical numbering and coding of imaginary transition structures. A novel approach to the linear coding of individual organic reactions. J. Chem. Inf. Comput. Sci. 1988, 28, 128-137. Several delimiters have been changed in the IUPAC name.
33. This discussion is quite subtle, since the diagrams produced by a sixheterov, a cyclohexanev, and a bzdrv skeleton are different in their conceptual levels. For example, the diagram produced by a cyclohexanev takes no account of vertices, while the diagram produced by a sixheterov considers that the vertices have carbons but no heteroatoms. Hence, we may consider that the three diagrams have the same appearance but can be regarded as being conceptually different. This discussion may conclude that a XyMML is unique and unambiguous to a structural diagram with consideration of any types of synonyms. It should be noted, however, that a XyMML has a nonunique and unambiguous nature with respect to a structure (not a diagram).
34. Goossens, M.; Mittelbach, F.; Samarin, A. The LaTeX Companion; Addison-Wesley: Reading, MA, 1994.
35. The DTD and related files will be obtained from the author's site, http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html.
36. The parser "sgmls" and the translator "sgmlsasp" have been developed by J. Clark and converted to accommodate Japanese characters by S. Tsuchiya. These tools have been obtained from NIFTY-serve, FPRINT forum, No. 135 (36SET.LZH).
37. The XyMTeX system (version 2.00) will be obtained from the author's site, http://www.chem.kit.ac.jp/fujita/fujitas/fujita.html.