Defining chemical definitions – Chemists Catherine Castillo-Colaux and Alain Krief of the University Notre-Dame de la Paix, Namur, Belgium, describe the different stages involved in the collaborative construction of an organic chemical ontology – a glossary of definitions and relationships – by chemists. Writing in the International Journal of Knowledge and Learning, they reveal their experiences, as chemists as opposed to computer scientists, in learning how to build a collaborative ontology and how to use the ontology software to do so. In so doing they show how chemists can work together on essentially computer science projects that benefit the chemistry community.

The chemists were working on building EnCOrE, a freely accessible net-based encyclopaedia of organic chemistry. They had selected what they thought to be adequate tools and strategies for transferring chemical knowledge into an electronic format but the whole process proved to be “far from easy”.

“The initial expectation that selected hypertext links would solve the problem proved to be inaccurate,” the researchers explain, “since those links were too numerous and too static. We also found that even the more elaborated XML language was inadequate, since we had too many interconnected contexts related to a single paragraph.”

The way forward was to adopt an ontological approach. An ontology, in the informatics and computing, as opposed to philosophical sense, is a formal explicit description of all the concepts in a given field. So an organic chemical ontology would include details of carbon, compounds, reactions, bonds, etc. An ontology contains Classes, or concepts, Slots, roles or properties, and Facets, role restrictions and together with a set of individual instances of classes, represents the sum of knowledge for the subject in question. It is the complete dictionary, taxonomy and semantics of the field formalised so that it is machine readable.

“We have been attracted by their efficiency to organise the inherent concepts within a domain or a subdomain and to ensure consistency between the different modules of our encyclopaedia,” the researchers explain.

The researchers outline the aches and pains they experienced in developing their ontology using various collaborative and Grid tools and ultimately the successes.

It took us quite a lot of time to become acquainted with and to understand ontology building. Our goal, as ‘chemists who are neophytes in ontology’ was not only to create an ontology of organic chemistry but also to find the important steps to enable ourselves as well as other chemists to be able to do so. It implies finding the best way to learn this new field.

Given the failures of certain approaches to ontology building, the team carefully analysed the different problems encountered and have devised a new protocol they say will help other chemists develop ontologies for their own purposes and in their own fields.

“This way, we believe, the chemist or the expert in general can work at his/her own rhythm and find the right support at the right moment,” the researchers say, “The success of this protocol indeed deals with its capacity to allow the participant to learn and at the same time to work. Use of the appropriate tool seems to be essential for success.”

Catherine Castillo Colaux, Alain Krief (2008). Protocols for building an organic chemical ontology International Journal of Knowledge and Learning, 4 (2/3) DOI: 10.1504/IJKL.2008.020652