Chemical Markup, XML and the World-Wide Web. Part III: Towards a Signed Semantic Chemical Web of Trust.

Georgios V. Gkoutos¹, Peter Murray-Rust², Henry S. Rzepa¹ and Michael Wright¹

(1) Department of Chemistry, Imperial College of Science, Technology and Medicine, UK - (2) School of Pharmaceutical Sciences, University of Nottingham, UK - November 29, 2000

We describe how a collection of documents expressed in XML-conforming languages such as CML and XHTML can be authenticated against digital signatures which make use established X.509 certificate technology. These can be associated either with specific nodes in the XML document or with the entire document. We illustrate this with two examples. An entire journal article expressed in XML has its individual components signed by separate authors, and the collection is placed in an envelope and again signed. The second example involves using a software robot agent to acquire a collection of documents from a specified URL, to perform various operations and transformations on the content, including expressing molecules in CML, to automatically sign the various components and deposit the result in repository. We argue that these operations can be used to build what we term a authenticated and semantic chemical web of trust.

Article: XML version (XSL) : XML Version (XSLT) : XHTML version : PDF version

Please note that these XML documents require Internet Explorer 5.0 or 5.5 (Windows) to display correctly. As yet, no other browsers have sufficient XSL support. XHTML versions are supplied (stylesheet transformed from their native XML) but may display incorrectly on some older browsers.

Two XML versions of the article are supplied. The first (XSL) uses the XSL stylesheet language supplied with Internet Explorer 5 and 5.5 (msxml2). This is not compliant with the XSLT recommendation produced by the W3C. The second (XSLT) version requires that IE be upgraded to the latest XML parser (msxml3). The process is as follows: download and install msxml3.exe, then download, unzip and run the xmlinst.exe utility. In both cases, please open your IE's 'Tools' menu and set /Internet Options/Security/Custom Level/Access data sources across domains/ to "Enable". Alternatively you can add http://www.ch.ic.ac.uk/chimeral/ and http://www.xml-cml.org/ to your trusted sites list.

Supplemental Materials

Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content, P. Murray-Rust, H. S. Rzepa and M. Wright, New. J. Chemistry, 2001, in press - XML version
A demonstration of how XML components can be signed by different authors. Correct display of this document requires the Adobe SVG and MDL Chime plugins. An external signature for this article can be found here.

Twist localisation in Single, Double and Triple Twisted Mobius Cyclacenes, Sonsoles Martin-Santamaria and Henry S. Rzepa, J. Chem Soc, Perkin Trans 2, 2000, 2378 - original article - XHTML version
This article was originally authored using HTML/Molfile, it was the converted to XHTML/CML using the ChemDig, JChemTidy and JChemMeta agents and signed.

Examples and Instructions - XML version - XHTML version
Examples of the technologies described in this article can be downloaded here (2.5 Mg zip).

Acknowledgement

One of us (GVG) thanks Merck Sharpe and Dohm and the EPSRC for the award of a studentship.