Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions

Journal of Chemical Information and Modeling

Volumn 46, Issue 1, 2006, Pages 145-157

  Holliday, Gemma L ^a   Murray Rust, Peter ^a   Rzepa, Henry S ^b  

^a Department of Engineering   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; EMITTER COUPLED LOGIC CIRCUITS; SEMANTICS; WORLD WIDE WEB; XML;

BIOCHEMICAL REACTIONS; CHEMICAL MARKUP; XMLSCHEMA;

COMPUTER AIDED ANALYSIS;

EID: 33244487238     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0502698     Document Type: Conference Paper

References (26)

1. Murray-Rust, P.; Rzepa, H. S. Chemical Markup, XML, and the World Wide Web. 4. CML Schema. J. Chem. Inf. Comput. Sci. 2003, 43, 757-772. DOI: 10.1021/ci0256541.
2. Wakelin, J.; Murray-Rust, P.; Tyrrell, S.; Zhang, Y.; Rzepa, H. S. CML Tools and Information Flow in Atomic Scale Simulations. Mol. Simul. 2005, 31, 315-322. DOI: 10.1080/08927020500065850.
3. Details can be found at the following URL: http://cml.sourceforge.net/ list/.
4. Ingold, C. K. Structure and Mechanism in Organic Chemistry, 2nd ed.; Cornell University Press: Ithaca, NY, 1969; Chapters 5-15.
5. As reviewed by Hendrickson, J. B.; Chen, L. The Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Clark, T., Gasteiger, L., Kollman, P. A., Schaefer, H. F., Scheriner, P. R., Eds.; J. Wiley & Sons: Chichester, U.K., 1998; Vol. 4, pp 2381-2402.
6. Valdutz, G. Modern Approaches to Chemical Reaction Searching; Willett, P., Ed.; 1986; Gower: London, pp 202-220.
7. (a) Chen, L. Handbook of Chemoinformatics; Gasteiger, J., Ed.; Wiley-VCH: 2003; pp 347-388.
8. (b) Hendrickson, J. B. Descriptions of reactions: their logic and applications. Recl. Trav. Chim. Pays-Bas 1992, 111, 323-334
9. Hendrickson, J. B. Comprehensive System for Classification and Nomenclature of Organic Reactions. J. Chem. Inf. Comput. Sci. 1997, 37, 852-860.
10. Hendrickson, J. B.; Miller, T. M. Reaction classification and retrieval. A linkage between synthesis generation and reaction databases. J. Am. Chem. Soc. 1991, 113, 902-910.
11. Hendrickson, J. B.; Sander, T. L. The systematic definition of organic reactions. Chem. Eur. J. 1995, 1, 449-453.
12. Arens, J. F. A formalism for the classification and design of organic reactions. I. The class of (-+)n reactions. Recl. Trav. Chim. Pays-Bas 1979, 98, 155-161.
13. A formalism for the classification and design of organic reactions. II. The classes of (+-)n+ and (-+)n- reactions. Recl. Trav. Chim. Pays-Bas 1979, 98, 395-399.
14. A formalism for the classification and design of organic reactions. III. The class of (+-)nC reactions. Recl. Trav. Chim. Pays-Bas 1979, 98, 471-500.
15. Zefirov, N. S.; Baskin, I. I.; Palyulin, V. A. SYMBEQ Program and Its Application in Computer-Assisted Reaction Design. J. Chem. Inf. Comput. Sci. 1994, 34, 994-999. DOI: 10.1021/ci00020a038.
16. (e) Ugi, I.; Bauer, J.; Bley, K.; Dengler, A.; Dietz, A.; Fontain, E.; Gruber, B.; Herges, R.; Knauer, M.; Reitsam, K.; Stain, N. Computer-assisted solution of chemical problems: a new discipline in chemistry. Angew. Chem., Int. Ed. 1993, 32, 201-221.
17. Ugi, I.; Bauer, J.; Blomberger, C.; Brandt, J.; Dietz, A.; Fontain, E.; Gruber, B.; Scholley-Pfab, A. v.; Sneff, A.; Stein N. Models, concepts, theories, and formal languages in chemistry and their use as a basis for computer assistance in chemistry. J. Chem. Inf. Comput. Sci. 1994, 34, 3-16. DOI: 10.1021/ci00017a001.
18. Murray-Rust, P.; Rzepa, H. S.; Tyrrell, S. M.; Zhang, Y. Representation and use of Chemistry in the Global Electronic Age. Org. Biomol. Chem. 2004, 2, 3192-3203. DOI: 10.1039/B410732.
19. Stein, S. E.; Heller, S. R.; Tchekhovski, D. An Open Standard for Chemical Structure Representation - The IUPAC Chemical Identifier, Nimes International Chemical Information Conference Proceedings, 2003, pp 131-143.
20. IUPAC Compendium of Chemical Terminology ("Gold book"); 2nd ed.; McNaught, A. D., Wilkinson, A., Eds; Blackwell Science: 1997.
21. Holliday, G. L.; Mitchell, J. B. O.; Murray-Rust, P. CMLSnap. A novel method of reaction representation. Internet J. Chem. 2004, 7, Article 4.
22. Krause, S.; Willighagen, E.; Steinbeck, C. JChemPaint - using the collaborative forces of the Internet to develop a free editor of 2D chemical structures. Molecules 2000, 5, 93-98. See, also: http://jchempaint.sourceforge. net/.
23. Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci. 2003, 43, 493-500. DOI: 10.1021/ci025584y See, also: http://cdk.sourceforge.net/
24. Murray-Rust, P.; Mitchell, J. B. O.; Rzepa, H. S. Chemistry in Bioinformatics. BMC Bioinformatics 2005, 6, 141, DOI: 10.1186/1471-2105-6-141.
25. P. Murray-Rust, P.; Rzepa, H. S. Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM. J. Chem. Inf. Comput. Sci. 2001, 41, 1113-1123. DOI: 10.1021/ci000404a.
26. Many examples of reaction animations can be found at http://www-mitchell. ch.cam.ac.uk/macie/.