Overcoming the ontology enrichment bottleneck with Quick Term Templates

  • Authors:

  • Philippe Rocca-Serra;Alan Ruttenberg;Martin J. O'Connor;Patricia L. Whetzel;Daniel Schober;Jay Greenbaum;Mé/lanie Courtot;Ryan R. Brinkman;Susanna Assunta Sansone;Richard Scheuermann;Richard Scheuermann;Bjoern Peters

  • Affiliations:

  • (Correspd. Tel.: +44 01865 610 657/ Fax: +44 01865 610 612/ E-mail: proccaserra@gmail.com) Oxford e-Research Centre, University of Oxford, Oxford, UK. E-mails: proccaserra@gmail.com, sa.sansone@gm ...;Science Commons, Cambridge, MA, USA. E-mail: alanruttenberg@gmail.com;Stanford University, Stanford, CA, USA. E-mails: martin.oconnor@stanford.edu, whetzel@stanford.edu;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;Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada. E-mails: mcourtot@gmail.com, rbrinkman@bccrc.ca;Oxford e-Research Centre, University of Oxford, Oxford, UK. E-mails: proccaserra@gmail.com, sa.sansone@gmail.com;Department of Pathology and Division of Biomedical Informatics, U.T. Southwestern Medical Center, Dallas, TX, USA. E-mail: richard.scheuermann@utsouthwestern.edu;The OBI Consortium;La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA. E-mails: bpeters@liai.org, jgbaum@gmail.com

  • Venue:
  • Applied Ontology - Biomedical Ontologies
  • Year:
  • 2011

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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.