SemanticEye: A semantic Web application to rationalize and enhance chemical electronic publishing

Journal of Chemical Information and Modeling

Volumn 46, Issue 6, 2006, Pages 2396-2411

  Casher, Omer ^a   Rzepa, Henry S ^b  

^a GLAXOSMITHKLINE   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); COMPUTER MUSIC; DATA STRUCTURES; ELECTRONIC DOCUMENT EXCHANGE; ELECTRONIC PUBLISHING; METADATA; WORLD WIDE WEB;

CHEMICAL INFORMATION; DIGITAL MUSIC MANAGEMENT; ONTOLOGY; SEMANTIC WEB APPLICATION;

SEMANTICS;

EID: 33845723240     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci060139e     Document Type: Article

References (48)

1. Tenopir, C.; King, D. W. Precis of 'Towards Electronic journals: realities for Scientists, Librarians, and Publishers', 2000. Psycoloquy. http://psycprints.ecs.soton.ac.uk/archive/00000084/#html (accessed Jan 23, 2006).
2. James, D.; Whitaker, B. J.; Hildyard, C.; Rzepa, H. S.; Casher, O.; Goodman, J. M.; Riddick, D.; Murray-Rust, P. The Case for Content Integrity in Electronic Chemistry Journals: The CLIC Project. New. Rev. Inf. Networking 1995, 1, 61-70.
3. Bachrach, S. M.; Burleigh, D. C.; Krassivine, A. Designing the Next-Generation Chemistry Journal: The Internet Journal of Chemistry. Issues Sci. Tech. Librarian [Online] 1998, 17, Article 1. http://www.library.ucsb.edu/ istl/98-winter/articlel.html (accessed Jan 28, 2006).
4. Goodman, J. M. Chemistry on the world-wide-web: a ten year experiment. Org. Biomol. Chem. 2004, 2, 3222-3225. DOI: 10.1039/b409956g.
5. Smith, J. W. T. The Deconstructed Journal - a New Model for Academic Publishing. Learned Publishing 1999, 12, 79-91.
6. Budapest Open Access Initiative, http://www.soros.org/openaccess (accessed Feb 2, 2006).
7. Ianl.arXiv.org e-Print archive mirror, http://xxx.Ianl.gov/ (accessed Feb 2, 2006).
8. Weller, A. C. Can editorial peer review survive in a digital environment? In ACS Division of Chemical Information (CINF), Proceedings of the 228th ACS National Meeting and Exposition, Philadelphia, PA, 2004. http://acscinf.org/ docs/meetings/228nm/presentations/228nm14.pdf (accessed Jan 16, 2006).
9. Murray-Rust, P.; Rzepa, H. S.; Stewart, J. J. P.; Zhang, Y. A global resource for computational chemistry. J. Mol. Model. 2005, 11, 532-541. DOI: 10.1007/s00894-005-0278-1.
10. DSpace Federation, http://www.dspace.org/ (accessed Feb 5 2006).
11. King, D. W.; Tenopir, C. 25 Year trends in information seeking and reading patterns of chemists. In ACS Division of Chemical Information (CINF), Proceedings of the 228th ACS National Meeting and Exposition, Philadelphia, PA, 2004. http://acscinf.org/docs/meetings/228nm/presentations/228nm05.pdf (accessed Jan 16, 2006).
12. Berners-Lee, T.; Hendler, J.; Lassila, O. The Semantic Web. Sci. Am. 2001, 5, 34-43.
13. Taylor, K. R.; Gledhill, R. J.; Essex, J. W.; Frey, J. G. Bringing Chemical Data onto the Semantic Web. J. Chem. Inf. Model. 2006, 46, 939-952. DOI: 10.1021/ci050378m.
14. Berners-Lee, T. The Semantic Web and Challenges, 2003. World Wide Web Consortium. http://www.w3.org/2003/Talks/01-sweb-tbl/ (accessed Feb 21, 2006).
15. Lassila, O.; Swick, R. Resource Description Framework (RDF) Model and Syntax Specification, 1999. World Wide Web Consortium, http://www.w3.org/TR/PR- rdf-syntax (accessed Feb 27, 2006).
16. Brennan, K.; Petrosillo, S. Demystifying the Semantic Web: Is Migration Right for You?, 2003. Creative Behavior, http://www.cre-ativebehavior.com/index. php?PID=87 (accessed Mar 5, 2006).
17. Howison, J.; Goodrum, A. Why can't I manage academic papers such as MP3s? The evolution and intent of Metadata standards. In Proceedings of Colleges, Code and Copyright, ACRL Publications in Librarianship no. 57, College Park, MD, 2004; ACRL: Chicago, 2005.
18. Adobe XMP: Adding Intelligence to Media, http://www.adobe.com/products/ xmp/ (accessed 28 May, 2004).
19. PRISM: Publishing Requirements for Industry Standard Metadata. http://www.prismstandard.org/ (accessed Feb 19, 2006).
20. Murray-Rust, P.; Mitchell, J. B. O.; Rzepa, H. S. Communication and re-use of chemical information in bioscience. BMC Bioinformatics [Online] 2005, 6, Article 180. http://www.ch.ic.ac.uk/rzepa/bmc2/ (accessed Dec 11, 2005). DOI: 10.1186/1471-2105-6-180.
21. The Digital Object Identifier System, http://www.doi.org/hb.html (accessed Feb 10, 2006). DOI: 10.1000/182.
22. IUPAC. http://www.iupac.org/projects/2000/2000-025-1-800.html (accessed Feb 12, 2006).
23. Broekstra, J.; Kampman, A.; van Harmelen, F. Sesame: A Generic Architecture for Storing and Querying RDF and RDF Schema. In Lecture Notes in Computer Science, Proceedings of the First International Semantic Web Conference, Sardinia, Italy, 2002; Horrocks, I., Hendler, J. A., Eds.; Springer: Berlin, 2002; pp 54-68.
24. Martín-Santamaría, S.; Carroll, M. A.; Pike, V. W.; Rzepa, H. S.; Widdowson, D. A. Fluoridation of Heteroaromatic Iodonium Salts: Experimental Evidence Supporting Theoretical Prediction of the Selectivity of the Process. J. Chem. Soc., Perkin Trans. 2 2000, 2, 2158-2161. DOI: 10.1039/b000429o.
25. Rzepa, H. S.; Sanderson, N. Aromaticity on the Edge of Chaos: An Ab initio study of the bimodal balance between aromatic and non-aromatic structures for 10-π-Dihetero[8]annulenes. Phys. Chem. Chem. Phys. 2004, 6, 310-313. DOI: 10.1039/b312724a.
26. Wiedenfeld, D. Remote functionalization by tandem radical chain reactions. J. Chem. Soc., Perkin Trans. 1 1997, 3, 339-347. DOI: 10.1039/a600172f.
27. Zielinska, A.; Skulski, L. A solvent-free synthesis of (dichloroiodo)-arenes from iodoarenes. Tetrahedron Lett. 2004, 45, 1087-1089. DOI: 10.1016/j.tetlet.2003.11.071.
28. Fujita, T.; Fuchigami, T. Electrolytic Partial Fluorination of Organic Compounds. 20.1 Electrosynthesis of Novel Hypervalent Iodobenzene Chlorofluoride Derivatives and Its Application to Indirect Anodic gem-Difluorination. Tetrahedron Lett. 1996, 37, 4725-4728. DOI: 10.1016/0040-4039(96)00951-3.
29. Prakash, O.; Kaur, H.; Pundeer, R.; Dhillon, R. S.; Singh, S. P. An Improved Iodine(III) Mediated Method for Thiocyanation of 2-Arylindan-1,3- diones, Phenols, and Anilines. Synth. Comm. 2003, 33, 4037-4042. DOI: 10.1081/SCC-120026343.
30. Filippou, A. C.; Winter, J. G.; Kociok-Köhn, G.; Troll, C.; Hinz, I.; Electron-Rich Trichlorogermyl Complexes of Molybdenum and Tungsten Bearing a Cyclopentadienyl Ligand: Synthesis, Crystal Structures, and Cyclic Voltammetric Studies. Organometallics 1999, 18, 2649-2659. DOI: 10.1021/om990101+.
31. Sawaguchi, M.; Ayuba, S.; Hara, S. A Practical Synthetic Method of Iodoarene Difluorides without Fluorine Gas and Mercury Salts. Synthesis 2002, 13, 1802-1803. DOI: 10.1055/s-2002-33913.
32. SciFinder. http://www.cas.org/SCIFINDER/scicover2.html (accessed Mar 8, 2006).
33. Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H. S.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. The Blue Obelisk - Interoperability in Chemical Informatics. J. Chem. Inf. Model. 2006, 46, 991-998. DOI: 10.1021/ci050400b.
34. Townsend, J. A.; Adams, S. E.; Waudby, C. A.; de Souza, V. K.; Goodman, J. M.; Murray-Rust, P. Chemical documents: machine understanding and automated information extraction. Org. Biomol. Chem. 2004, 2, 3294-3300. DOI: 10.1039/b411033a.
35. Gkoutos, G. V.; Murray-Rust, P.; Rzepa, H. S.; Wright, M. Chemical Markup, XML and the World-Wide Web. Part III: Towards a signed semantic Chemical Web of Trust. J. Chem. Inf. Comput. Sci. 2001, 41, 1124-1130. DOI: 10.1021/ci000406v.
36. IETF/W3C XML-DSig Working Group. http://www.w3.org/Signature/.
37. Carroll, J. J.; Bizer, C.; Hayes, P.; Stickler, P. Named Graphs, Provenance and Trust. In International World Wide Web Conference, Proceedings of the 14th International Conference on World Wide Web, Chiba, Japan, 2005; Ellis, A., Hagin, T., Eds.; ACM Press: New York, U.S.A., 2005; pp 613-622. DOI: 10.1145/1060745.1060835.
38. Open Archives Initiative, http://www.openarchives.org/ (accessed Mar 25, 2006).
39. De Roure, D. Semantic Grid, http://www.semanticgrid.org/ (accessed Mar 14, 2006).
40. Brown, M. C. What is the semantic grid?, 2005. IBM developerWorks.
41. http://www-128.ibm.com/developerworks/grid/library/gr-semgrid/ (accessed Mar 14, 2006).
42. Wikimedia Meta-Wiki - RDF Metadata, http://meta.wikimedia.org/wiki/ RDF_metadata (accessed Mar 29, 2006).
43. Wikipedia. http://en.wikipedia.org/wiki/WikiWiki (accessed Mar 29, 2006).
44. Wikimedia Meta-Wiki - RDF. http://meta.wikimedia.org/wiki/RDF (accessed Mar 29, 2006).
45. Campanini, S. E.; Castagna, P.; Tazzoli, R. Platypus Wiki: A Semantic Wild Wiki Web. Presented at the 1st Italian Semantic Web Workshop. [Online], Ancona, Italy, 2004; Semantic Web Applications and Perspectives (SWAP), http://semanticweb.deit.univpm.it/swap2004/ (accessed Mar 27, 2006).
46. Hepp, M.; Bachlechner, D.; Siorpaes, K. OntoWiki: Community-driven Ontology Engineering and Ontology Usage based on Wikis. In International Symposium On Wikis, Proceedings of the 2005 International Symposium on Wikis, San Diego, CA, 2005; Riehle, D., Ed.; ACM Press: New York, 2005.
47. Chemistry - Wikipedia, the free encyclopedia. http://en.wikipedia.org/ wiki/Chemistry (accessed Mar 30, 2006).
48. Marshall, C. C.; Shipman, F. M. Which Semantic Web? In Conference on Hypertext and Hypermedia, Proceedings of the 14th ACM Conference on Hypertext and Hypermedia, Nottingham, U.K., 2003; Ashman, H., Brailsford, T., Carr, L., Hardman, L., Eds.; ACM Press: New York, 2003; pp 57-66. DOI: 10.1145/900051.900063.