UGRIC

Universal Generalised Information for Chemistry

Introduction

One of the main difficulties in production electronic articles is that the data is not available in a useful electronic form. Authors are keen to have 'enhanced articles' provided that no extra effort on their part is required. How can this fundamental problem be addressed?

In the original CLIC proposal this problem was assigned to Cambridge. We have been looking at protocols to integrate the way that experimental data is handled within the chemistry department. This work will focus on implementing authoring tools for laboratory data management at the bench chemist level. It must be seen to be in chemists interests to computerise their data at an early stage.

Initial work in this area has been exploring the use of SGML/XML and Java in the production of viewing and authoring tools. We have provisionally called this way of ordering data 'Ugric'. A more advanced approach in this area is Peter Murray-Rust's CML

A viewer has been written that can read the present of Ugric and display the contents in a browsable manner. An example of this applet can be found in db.html.

An applet has been written with the goal of an online submission for mass spectrometry. The idea behind this applet is to create an Ugric file containing all the relevant details for the spectrometrist. The Ugric file could then be incorporated into a larger Ugric database containing other details about the experimental. An example of this applet can be found in ms.html

Using this applet will make Mass spectrometry submission easier as the molecular weight and formula are calculated automatically. This should provide an incentive for building a machine readable database of chemical information which in turn should lead to enhanced articles without pain.

Other tools based on this technology are envisaged to enable the production of an electronic notebook. The notebook will be instantly browsable on the Internet and allow the extraction of relevant data in the correct form for production of papers or thesis with the minimum of effort.

Tools to convert between Ugric and other databases such as ISISbase and FileMaker Pro are being investigated.

The DTD for Ugric is extremely simple. This should make Ugric easier to convert to other database formats and at a very basic level allow browsing the Ugric file in a text editor. DTD v 1.0 can be found on ugricdtd.html This is an example of XML

Authoring tools designed to make the production of Ugric databases easier is also being explored see perl.html

All software can be downloaded from here

Daniel Chapman and Jonathan Goodman