Biomedical Ontology Integration


Barry Smith and Cornelius Rosse, “The Role of Foundational Relations in the Alignment of Biomedical Ontologies”, in M. Fieschi, et al. (eds.), Medinfo 2004, Amsterdam: IOS Press, 444–448.

Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan Rector, Cornelius Rosse, “Relations in Biomedical Ontologies”, Genome Biology, 2005, 6 (5), R46.

Anand Kumar, Yum Lina Yip, Barry Smith, Pierre Grenon, “Bridging the Gap between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma”, Computers in Biology and Medicine, 2006; 36, (7-8): 694-711.

Jean-Luc Verschelde, Mariana Casella Dos Santos, Tom Deray, Barry Smith and Werner Ceusters, “Ontology Assisted Database Integration to Support Natural Language Processing and Biomedical Data-Mining”, Journal of Integrative Bioinformatics, 1 (2003), 1-10; reprinted in R. Hofestädt (ed.), Yearbook of Bioinformatics (2004), 39-48.

Werner Ceusters, Barry Smith and James Matthew Fielding, “LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration”, in Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994), Berlin: Springer, 2004, 124–139.

James M. Fielding, Jonathan Simon, Werner Ceusters and Barry Smith, “Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration”, Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004, 114-120.

Jonathan Simon, James Fielding, Mariana Dos Santos and Barry Smith, “Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases”, International Journal of Medical Informatics, 75 (3-4), 2005, 224-231.

Jonathan Simon, James Matthew Fielding and Barry Smith, “Using Philosophy to Improve the Coherence and Interoperability of Applications Ontologies: A Field Report on the Collaboration of IFOMIS and L&C”, in Gregor Büchel, Bertin Klein and Thomas Roth-Berghofer (eds.), Proceedings of the First Workshop on Philosophy and Informatics. Deutsches Forschungszentrum für künstliche Intelligenz, Cologne: 2004, 65–72.

Barry Smith,  Michael Ashburner,  Cornelius Rosse,  Jonathan Bard,  Wil­liam Bug,  Werner Ceusters,  Louis J. Goldberg,   Karen Eilbeck,  Amelia Ireland,  Christopher J Mungall,  The OBI Consortium,  Neocles Leontis,  Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah,  Patricia L. Whetzel,  Suzanna Lewis, “The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology, 25 (11), November 2007, 1251 -1255.

Cornelius Rosse, Anand Kumar, Jose Leonardo V. Mejino, Daniel L. Cook, Landon T. Detwiler and Barry Smith, “A Strategy for Improving and Integrating Biomedical Ontologies”, Proceedings of AMIA Symposium 2005, Washington DC, 639–643.

Barry Smith, Werner Ceusters, Anand Kumar and Cornelius Rosse, “On Carcinomas and Other Pathological Entities”, Comparative and Functional Genomics, vol. 6, issue 7/8, 2005, 379–387.