title: The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Microarray Informatics Team, The European Bioinformatics Institute--European Molecular Biology Laboratory Outstation, Wellcome Trust Genome Campus CB10 1SD, Cambridge Hinxton, UK. a.garcia@imb.uq.edu.au
authors.forename: Alexander Garcia
authors.initials: AG
authors.lastname: Castro
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
authors.forename: Robert
authors.initials: R
authors.lastname: Stevens
authors.forename: Chris
authors.initials: C
authors.lastname: Taylor
authors.forename: Karim
authors.initials: K
authors.lastname: Nashar
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ragan
authors.forename: Susanna-Assunta
authors.initials: SA
authors.lastname: Sansone
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D016208:Databases, Factual; D023281:Genomics / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D009747:Nutritional Physiological Phenomena; D009626:Terminology as Topic