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Organization


 

The organizers of this workshop come from different backgrounds and are connected with researchers and clinicians from different areas in the vaccine/drug domain. The organizers will ensure that the workshop be relevant to international audiences from both industry and academia. ICBO attendees are expected to have considerable expertise in ontology development and applications.

 

Chairs:

Program committee (PC) Members:

 

 

Introduction of workshop chairs:

1. Yongqun “Oliver” He, DVM, PhD
Associate Professor
Department of Microbiology and Immunology
Unit for Laboratory Animal Medicine
Center for Computational Medicine and Bioinformatics
University of Michigan Medical School
018 ARF, 1150 W. Medical Center Dr.
Ann Arbor, MI 48109-5614, USA
Email: yongqunh@med.umich.edu

Dr. He is a domain expert in vaccine R&D and vaccine adverse events. Dr. He’s group has developed a web-based vaccine research and analysis system VIOLIN (http://www.violinet.org). Dr. He founded and is a primary developer of the Vaccine Ontology (VO) and the Ontology of Adverse Events (OAE). Dr. He’s laboratory also conducts wet-lab research to study host-Brucella interaction mechanisms and develop effective and safe Brucella vaccines. As the lead guest editor, Dr. He successfully co-organized a “special issue on vaccine informatics” in the Journal of Biomedicine and Biotechnology (http://www.hindawi.com/journals/jbb/si/vacin/). He also actively participates in the development of other ontologies including the Ontology for Biomedical Investigations (OBI) and Infectious Disease Ontology (IDO). Dr. He’s group plays a primary role in developing several ontology-oriented software programs such as OntoFox (http://ontofox.hegroup.org) for importing and reusing individual ontology terms, and Ontobee (http://www.ontobee.org) for ontology term information retrieval and display. His group is also applying and developing ontology-based literature mining tools to study biological pathways with an emphasis on vaccine-induced immune response networks.  

2. Luca Toldo, PhD
Principal Scientist
Knowledge Management
Merck KGaA
250, Frankfurterstrasse
64293 Darmstadt - Germany
Email: luca.toldo@merckgroup.com   

Dr. Toldo graduated from the Swiss Federal Institute of Technology Zurich (ETH Zürich), worked at the U.S. National Cancer Institute at Frederick (NCI-Frederick), Weizmann Institute, and at the European Molecular Biology Laboratory (EMBL). He joined Merck KGaA in 1997. He wrote a patent in knowledge discovery, and has publications in bioinformatics, biomedical ontologies and molecular modeling. Dr. Toldo’s current focus is on hypothesis generation and validation, through information extraction and formal reasoning. He is interested in literature mining of adverse drug events (ADE) and causal analysis of various ADEs. Dr. Toldo is member of AMIA, ASIS and IUCR, reviewer of several journals, and Expert at the European Commission.

3. Gully Burns, PhD
Project Leader
Information Sciences Institute,
Marina del Rey Chair,
Knowledge Engineering Working Group, BIRN
4676 Admiralty Way, Suite 1001,
Marina del Rey, CA 90292, USA
Email: gullyburns@gmail.com

Dr. Burns is a project leader and head of the biomedical knowledge engineering group at the Information Sciences Institute (ISI) in Marina del Rey California. As a researcher with an applied biomedical focus in an institute with a reputation in cutting edge Artificial Intelligence (AI) research, Gully focuses on constructing models that express the essential elements of biomedical knowledge in a form that may then be addressed with AI methods. This includes work on biocuration that leverages Natural Language Processing, information integration over multiple data sources and non-standard approaches to ontology engineering. Dr Burns is the originator of the “Knowledge Engineering from Experimental Design” (KEfED) methodology, has focused heavily on the study of neural connectivity in neuroinformatics but is currently broadening the focus of his approach to other fields. In particular he is working in collaboration with the SIV/HIV Vaccine Trial Database at Los Alamos National Laboratory and the National Primate Research Centers to apply the KEfED model to SIV/HIV Vaccine studies. He is spearheading an initiative at ISI in developing systems for discovery informatics called “Building a Breakthrough Machine”.

4. Cui Tao, PhD
Assistant Professor of Medical Informatics
Department of Health Sciences Research
Mayo Clinic College of Medicine
200 First Street, SW
Rochester, MN 55905, USA
Email: tao.cui@mayo.edu

Dr. Cui Tao is an expert in medical informatics with focus on ontologies, standard terminologies, and the semantic web. Dr. Tao is the PI of the CNTRO project (http://cntro.org), which focuses on representing, extracting, and reasoning of temporal relations in clinical data. She is in particular interested in the event modeling and time analysis of vaccine/drug adverse events.  She is also a co-investigator in many US federal funded projects including: SHARP (Strategic Health IT Advanced Research Projects) area 4 on Secondary Use of EHR Data, NCBO (National Center for Biomedical Ontologies), and PGRN (Pharmacogenomics Research Network).  Dr. Tao serves as a subject matter expert in NCI (National Cancer Institute)'s caBIG Vocabulary Knowledge Center.  She has served as a program committee member and reviewer in many Computer Science and medical informatics conferences and journals. She is the chair of the first international workshop of Managing Interoperability and compleXity in Health Systems (MIXHS, http://informatics.mayo.edu/CNTRO/index.php/Events/MIXHS11).   

5. Darrell R. Abernethy, MD, PhD, FACP
Associate Director for Drug Safety
U.S. Food and Drug Administration (FDA)
Professor of Medicine and of Pharmacology
Johns Hopkins School of Medicine
Email: Darrell.Abernethy@fda.hhs.gov 

Dr. Abernethy has more than 25 years of experience in medicine and pharmacology, including positions in academia, practice and research. He is Board Certified in Internal Medicine and Clinical Pharmacology. Dr. Abernethy has published over 200 peer reviewed original research publications. His studies of mechanisms of peripheral distribution of drugs, drug disposition, their effects in obesity, and pharmacokinetic/pharmacodynamic relationships of cardiovascular drugs in aging have been well received, and led to his being named to the ISI Most Highly Cited Researchers in Pharmacology. At FDA, Dr. Abernethy is responsible for leading the development of a pharmacological mechanism based safety program in the Office of Clinical Pharmacology to work in synergy with efforts in the Office of Surveillance and Epidemiology and other Offices and Centers at FDA. In addition to his work at FDA, he is currently a professor of medicine (geriatrics) and of pharmacology and molecular science (part–time) at the Johns Hopkins University School of Medicine.

 

 

 

Organizers

Yongqun"Oliver" He
University of Michigan

Luca Toldo
Merck KGaA

Gully Burns
Information Sciences Institute

Cui Tao
Mayo Clinic

Darrell R. Abernethy
USA FDA

 
News

30 April 2012: Workshop papers submission deadline.

15 May 2012: Notification of workshop paper acceptance.

30 June 2012: Camera-ready copies submission deadline.

21-22 July 2012: Workshop starts.

Maintainer: Oliver He