Open Access Highly Accessed Methodology article

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case

Alexander Garcia Castro1234, Philippe Rocca-Serra1, Robert Stevens5, Chris Taylor1, Karim Nashar5, Mark A Ragan23 and Susanna-Assunta Sansone1*

Author affiliations

1 Microarray Informatics Team, The European Bioinformatics Institute – European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK

2 Australian Research Council Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland 4072, St Lucia, Australia

3 Institute for Molecular Bioscience, The University of Queensland 4072, Brisbane, Australia

4 Australian Centre for Plant Functional Genomics, The University of Queensland 4072, Brisbane, Australia

5 School of Computer Science, University of Manchester, Kilburn Building, Oxford Road Manchester M13 9PL, Manchester, UK

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Citation and License

BMC Bioinformatics 2006, 7:267  doi:10.1186/1471-2105-7-267

Published: 25 May 2006



Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies.


Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer.


The contributions of this paper are the thorough description of the steps we suggest when building an ontology, example use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process.