Buffalo-Columbia workshop on

ontology and cancer bioinformatics

Friday, October 14

280 Park Hall, North Campus, University at Buffalo




  8.30                Continental Breakfast

  9.00                Aris Floratos: caWorkbench: Towards caBIG Interoperability

  9.45                Barry Smith: Ontology and the caBIG

10.30                Coffee

11.00                James J. Cimino: The Columbia/New York Presbyterian Medical Entities Dictionary

11.45                Lunch

12.45                Yves A.  Lussier: Bio-ontologies and Database Integration

13.30                Werner Ceusters: Tracking Tumors

14.15                Coffee followed by Brainstorming

18.30                Dinner




Werner Ceusters is Executive Director of the European Centre for Ontological Research. After studying medicine, neuropsychiatry, informatics and knowledge engineering he initiated a series of international research projects in medical natural language processing under the Third, Fourth and Fifth Research Frameworks of the European Commission and has also been active in standardisation bodies related to medical terminology such as CEN/TC251/WG2 and ISO/TC215/WG3. In April 1998, he started the company Language & Computing nv (L&C) to exploit the results of his research. He left L&C in 2004, his main interest being now applying and testing a new theoretically-grounded approach to ontological engineering, collaborating closely with the University at Buffalo.

James J. Cimino is Professor of Biomedical Informatics and Medicine Columbia College of Physicians and Surgeons. He is principal investigator on a National Library of Medicine Independent Investigator Grant to explore ways of addressing clinicians’ information needs.  He has over 190 publications, including 31 first-authored papers in peer-reviewed medical informatics journals. He contributed to the initial development of the Unified Medical Language System (UMLS) and his current research involves controlled medical vocabularies for medical decision support and the use of Internet resources to support patient care. 

Aris Floratos is currently serving as the Director of the Integrated Genomics Core at Columbia University. Before joining Columbia he was the Vice President of Computational Biology and Bioinformatics at First Genetic Trust, where he was a principal architect of software systems used in pharmacogenomic research and clinical trials. Prior to that, he was a research staff member at IBM’s T.J. Watson Research Lab, Life Science Division, where he worked on the applications of data mining approaches in the analysis of genomic data.

Yves A. Lussier is Director of the Biomedical Informatics Core of the Northeast Research Center of Excellence in Emerging Infectious Diseases, and Clinical Director of the Columbia Center for Advanced Technology. His research focuses on the use of computational medicine technologies to accurately individualize the understanding, prediction and treatments of diseases. More specifically, he has developed computational methods bringing together ontologies, NLP, artificial intelligence and heterogeneous data integration to analyze an increasingly large and complex wealth of clinical, genomic, and molecular databases.

Barry Smith is Julian Park Distinguished Professor of Philosophy in the University at Buffalo and Director of the Institute for Formal Ontology and Medical Information Science in Saarbrücken, Germany. His primary research focus is ontology and its applications in biomedicine and biomedical informatics, where he is working on a variety of projects relating to terminologies and electronic health records. He also collaborates with Hernando de Soto, Director of the Institute for Liberty and Democracy in Lima, Peru, on the ontology of economics and law.