Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface.
Esther R Rousay, Hongchen Fu, Jamie M Robinson, Jeremy G Frey, Jonathan W Essex
School of Chemistry, University of Southampton,
Highfield, Southampton, SO17 1BJ, UK

Abstract The Publication@Source Paradigm and Challenges Body Molecular Dynamics Simulations Comparisons and Conclusions Acknowledgements Appendix:The TriScapeRDF browser References Glossary Search
Introduction Introduction .2 Introduction .3 Introduction .4 Implementation of Publication@Source Implementation of Publication@Source .2 Implementation of Publication@Source .3 Implementation of Publication@Source .4

Implementation of Publication@Source .2

To achieve the aims of the publication@source project, we need to solve two problems: one is about how to describe the experimental and analysis processes and another one is to display the record of the processes applied to the data. We use semantic technologies, namely RDF (resource description framework) and an ontology to record the processes16. The ontology is used to define the vocabularies that describe the experimental and analysis processes to facilitate the sharing of information among collaborators in different organisations. This RDF description needs to serve two aims: to record the necessary information for presentation in a human readable logbook and to provide a workflow that can be automatically enacted. The need to represent the wide range of chemical objects such as pictures, figures, videos, mathematical formulae, chemical structures etc. can fortunately be achieved by using XML-based technologies, e.g. XML for structured data and text (http://www.w3.org/XML/), SVG (scalable vector graphics http://www.w3.org/Graphics/SVG/32) for pictures and figures, MathML (Mathematical Makeup Language http://www.w3.org/Math/) and CML (Chemical Makeup Language http://www.xml-cml.org/).

Many of the figures are plotted in the SVG format by the iSVG (interactive SVG) utility that simplifies the provision of hyper links to each data point on a graph. For example, for the polarisation data shown in figure 7, a link is provided from each data point back to raw the data (data from 2000 laser shots) from which the mean and error bar were calculated. This raw data is dynamically pulled from the database, based on a URI stored in the RDF description, which directs a web service to resolve the request as an SQL request to the database, and then recalculate the average of the points delivered. The RDF representation captures the fact that each step in the analysis process is performed according to a model, and allows for additional assumptions (parameters) to be included and comments to be made about each step. These comments can subsequently be rendered to provide the explanation of the model used at each step. The simplified data analysis tracking represented in this work considers largely linear data flows. The TriScape browser can display branching links but the current menu system does not provide an ideal view in these cases; this restriction will be lifted in the next version of the TriScape Browser. The RDF structures are interpreted using the TriScape ?browser?, a JAVA server application (running under Tomcat), which resolves the RDF references and renders the extracted information in HTML. The raw RDF is viewable in a separate window. More details about the TriScape browser are given in the appendix.


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