Issue title: Biomedical Ontologies
Article type: Research Article
Authors: Rocca-Serra, Philippe; | Ruttenberg, Alan | O'Connor, Martin J. | Whetzel, Patricia L. | Schober, Daniel | Greenbaum, Jay | Courtot, Mélanie | Brinkman, Ryan R. | Sansone, Susanna Assunta | Scheuermann, Richard | The OBI Consortium, | Peters, Bjoern
Affiliations: Oxford e-Research Centre, University of Oxford, Oxford, UK. E-mails: proccaserra@gmail.com, sa.sansone@gmail.com | Science Commons, Cambridge, MA, USA. E-mail: alanruttenberg@gmail.com | Stanford University, Stanford, CA, USA. E-mails: martin.oconnor@stanford.edu, whetzel@stanford.edu | Institute for Medical Biometry and Medical Informatics, University Clinic, Freiburg, Germany. E-mail: schober@imbi.uni-freiburg.de | La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA. E-mails: bpeters@liai.org, jgbaum@gmail.com | Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada. E-mails: mcourtot@gmail.com, rbrinkman@bccrc.ca | Department of Pathology and Division of Biomedical Informatics, U.T. Southwestern Medical Center, Dallas, TX, USA. E-mail: richard.scheuermann@utsouthwestern.edu
Note: [] Corresponding author: Philippe Rocca-Serra, Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK. Tel.: +44 01865 610 657; Fax: +44 01865 610 612; E-mail: proccaserra@gmail.com.
Abstract: When developing the Ontology of Biomedical Investigations (OBI), the process of adding classes with similar patterns of logical definition is time consuming, error prone, and requires an editor to have some expertise in OWL. Moreover, the process is poorly suited for a large number of domain experts who have limited experience with ontology development, and this can hinder contributions. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions, yet requires minimal manual intervention by the OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format that is subsequently converted into an OWL file. This procedure promises to be a robust and scalable approach for ontology enrichment as evidenced by encouraging results obtained when evaluated with an early version of the MappingMaster Protégé plugin.
Keywords: Quick Term Template, ontology coverage, Ontology for Biomedical Investigations, pattern, MappingMaster Protégé plugin
DOI: 10.3233/AO-2011-0086
Journal: Applied Ontology, vol. 6, no. 1, pp. 13-22, 2011
