Chemical markup, XML, and the world wide web. 5. Applications of chemical metadata in RSS aggregators

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 2, 2004, Pages 462-469

  Murray Rust, Peter ^a   Rzepa, Henry S ^b   Williamson, Mark J ^b   Willighagen, Egon L ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; DATA STRUCTURES; METADATA; MOLECULAR PHYSICS; SPECIFICATIONS; WORLD WIDE WEB; XML;

CHEMICAL MARKUP LANGUAGE; MOLECULAR MATRIX;

CHEMISTRY;

EID: 1842740220     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci034244p     Document Type: Article

References (26)

1. Berners-Lee, T.; Hendler, J. Publishing on the semantic Web. Nature 2001, 410, 1023-4.
2. Murray-Rust, P.; Rzepa, H. S. Scientific publications in XML - toward a global knowledge base. Data Sci. 2002, 1, 84-98.
3. Murray-Rust, P.; Rzepa, H. S. The Next Big Thing: From Hypermedia to Datuments. J. Digital Information 2004, in press. For a reprint, see http://www.ch.ic.ac.uk/rzepa/jodi/.
4. Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electrnic Mail and World Wide Web information exchange. J. Chem. Inf. Comput. Sci. 1998, 38, 976-982. See also http://www.ch.ic.ac.uk/chemime/.
5. Proceedings of the Electronic Conference on Trends in Heterocyclic Chemistry (ECHET96), Rzepa, H. S., Snyder, J., Leach, C., Eds.; ISBN 0-85404-894-4; CD ROM Version, The Royal Society of Chemistry. 1997. See also http://www.ch.ic.uk/ectoc/.
6. The term intertwingling was coined for this process by Ted Nelson in his own far sighted vision encapsulated in the Xanadu project, now reincarnated as Zig-Zag: http://xanadu.com/zigzag/.
7. Hammond, A. Why Choose RSS 1.0. http://www.xml.com/pub/a/2003/07/23/rssone.html.
8. See http://www.prismstandard.org/.
9. Murray-Rust, P.; Rzepa, H. S. Towards the Chemical Semantic Web. An introduction to RSS. Internet J. Chem. 2003, 6, article 4.
10. For formal recommendations, see http://www.w3.org/TR/REC-xmlnames/.
11. RDF Site Summary (RDF); http://www.w3.org/2000/08/w3c-synd/.
12. For an RSS validation service, see http://feedvalidator.org/.
13. Rzepa, H. S.; Williamsn, M. J. Chemstock: A Web-based Chemical Inventory system built from OpenSourceSoftware Components. Internet J. Chem. 2002, article 6. For a reprint, see http://www.ch.ic.ac.uk/csdemo/article/.
14. Murray-Rust, P.; Rzepa, H. S. Chemical Markup, XML and the Worldwide Web. Part 4. CML Schema. J. Chem. Inf. Comput. Sci. 2003, 43, 757-772 and references therein. See also http://cml.sourceforge.net/.
15. See http://openbabel.sourceforge.net/.
16. Linstrom, P. J.; Tchekhovskoi, D. V. Transitioning to a structure based identification system. Abstr. Papers, 226th ACS National Meeting, New York, United States, September 7-11, 2003, CINF-085. See also http://www.iupac.org/projects/2000/2000-025-1-800.html.
17. For information about RSS Writer see http://usefulinc.com/rss/rsswriter/.
18. Willighagen, E. L.; Josten, G.; Fleuren, M. http://www.woc.sci.kun.nl/.
19. World Wide Molecular Matrix (WWMM), http://wwmm.ch.cam.ac.uk/.
20. Stewart, J. J. P. MOPAC: a semiempirical molecular orbital program. J. Comput. Aided Mol. Design 1990, 4, 1-105. See also http://www.cachesoftware.com/mopac.
21. For information about Jmol, see http://jmol.sourceforge.net/.
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(1), 93-98. See also http://jchempaint.sourceforge.net/.
23. Steinbeck, C.; Han, Y.; 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.
24. Willighagen, E. L. Processing CML conversions in Java. Internet J. Chem. 2001, 4, article no. 4.
25. Rzepa, H. S.; Murray-Rust, P. A New Publishing Paradigm: STM Articles as part of the Semantic Web. Learned Publishing 2001, 14, 177.
26. The relevant module (rssviewer.jar) is available via the CDK site: http://cdk.sourceforge.net/.