VDOSME image

Call for papers


Vaccines and drugs have been critical to prevent and treat human and animal diseases. Vaccines and drugs are closely related in various aspects such as preclinical research and development, manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring.


In a broader scope, vaccine is a special type of drug. Vaccines and chemical drugs have also many differences. For example, for vaccines, dose, time, route, and frequency of administration are generally known quite precisely. However, dose, time, and frequency of drug administration are often very difficult to establish. Since vaccines are often administered to healthy people to prevent disease, attribution of an adverse event following vaccination is less likely to be confounded by signs or symptoms of underlying disease. However, separation of manifestation of disease from manifestation of drug effect is often very challenging. In the U.S.A, vaccines are regulated under different laws by the Center for Biologics (CBER) at FDA, while drugs are regulated under the Food Drug and Cosmetic Act by the The Center for Drug Evaluation and Research (CDER) at FDA. Safety surveillance for vaccines is for the most part carried out by the Center for Disease Control (CDC) in Atlanta, while for drugs it is carried out by the FDA. Due to these similarities and differences between vaccines and chemical drugs, a closer communication between these two areas is important to create effective ontological frameworks around which we can build comparative and predictive systems for both vaccines and drugs.

Although several related ontologies have been initiated with much progress made in the recent years, we still face many challenges in order to fully and logically represent vaccines and drugs and efficiently use the ontologies. In the case of ontology representation, no consensuses have been achieved on how to ontologically represent many relevant areas, for example:

  • Vaccine and drug administration dose, route, and frequency,
  • Drug-drug interactions, drug-food interactions, and how they affect vaccine and drug adverse events,
  • Experimental testing and analysis of vaccine/drug-induced immune responses, and
  • The complexity of time constraints for clinical events post vaccination or medication.

Meanwhile, it is also a challenge to efficiently apply biomedical ontologies to solve research and clinical problems. For example:

  • Is it possible to apply ontologies for advanced literature mining in order to discover new gene interaction networks underlying protective/therapeutic immune responses or vaccine and drug adverse events?
  • How to apply ontologies for personalized medicine?
  • How to use ontologies to improve the performance of complex vaccine/drug research and clinical data analysis?

As exemplified here, this workshop aims to identify, propose, and discuss solutions for important research problems in ontology representation and analysis of vaccine and drug formation and preparation, administration, function mechanisms, and induced host immune responses. The immune responses can be positive responses for prevention and/or treatment of a disease, or can be negative responses, i.e., adverse events. This workshop is expected to support the deeper understanding of vaccine and drug mechanisms and effects.

We welcome paper submissions in the above listed areas. More specific topics will be selected based on attendees’ submissions and interests.

It is noted that this workshop (VDOSME) will be coordinated with another proposed workshop titled “Methods for adverse events representation - Ontology and Information Model”. The other workshop targets various adverse events, including not only vaccine and drug adverse events, but also other adverse events such as medical device and surgery-associated adverse events. Their workshop focuses on ontology/information models for adverse events primarily in the “clinical” space (where information models already exist). Our VDOSME workshop targets various topics in the domain of vaccine and drug, which goes beyond adverse events. With respect to the adverse event domain, the VDOSME workshop proposal has a focus on “research” (in contrast to “clinical” space) of adverse event mechanisms, for example, modeling and analysis of gene-gene and drug-gene interactions, pathways, and host immune responses. These research topics can be studied by different approaches including literature mining and meta-analysis. When you submit your paper, please consider which workshop is more appropriate for you. You may also consider submitting papers to both workshops. It is likely that these two workshops will be held at different days. Therefore, you have a chance to attend both workshops.

This workshop is expected to be extremely useful to designers and implementers of drug and vaccine related ontologies in large and complex enterprise, nationwide clinical data repositories, electronic health systems for vaccine and drug safety analysis and new development.

For the information about how to prepare and submit your manuscript for consideration in the VDOSME 2012 workshop, please go to the VDOSME Submission page.


Selective full-length papers accepted in this workshop will be invited to extend the workshop papers and be included in a special issue as a thematic series in the Joural of Biomedical Semantics. We believe that the eventual inclusion of accepted full-length publication in the special issue will stimulate more submissions of high quality manuscripts.



Yongqun"Oliver" He
University of Michigan

Luca Toldo
Merck KGaA

Gully Burns
Information Sciences Institute

Cui Tao
Mayo Clinic

Darrell R. Abernethy


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