Studies on vaccine and drug mechanisms and effects using biomedical ontologies

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Guest blog post by Yongqun He, who is series editor for the newly launched “Vaccine and Drug Ontology in the Study of Mechanism and Effect” (VDOSME) thematic series. The VDOSME workshop provides a platform for discussing problems and solutions in the development and application of biomedical ontologies to representing and analyzing vaccines and drugs. In this blog post he explores how the cutting-edge research published in this series makes a valuable contribution to the field.

Vaccines and drugs have contributed to dramatic improvements in public health worldwide. Although therapeutic vaccines are being invented, vaccines are classically administered to prevent the appearance of a medical problem. Chemical drugs are generally administered to treat a medical problem. Nevertheless, vaccines and chemical drugs are similarly regulated both in research and development, manufacturing, clinical trials, government approval and regulation, and post-licensing usage surveillance and monitoring. In a broader scope, vaccine is a special type of drug.

It is challenging but critical to study the mechanisms and effects of vaccines and drugs. The fundamental understanding of the mechanisms and effects is important to rationally design vaccines and drugs and avoid adverse effects in the host. The effects of the administration of a vaccine and drug include two sides: positive desired host response and negative undesired adverse host response (i.e., adverse effect). An adverse event is a pathological bodily response that occurs after a vaccine or drug administration and is adverse to the intention of the vaccine and drug usage. An adverse event may or may not be caused by administration of the vaccine or drug. An adverse event that is caused by administration of a vaccine or drug administration is called a causal adverse event or adverse effect of a vaccine or drug. How to identify the causal relationship between a vaccine/drug administration and host response has been a topic of intensive research. Many factors may be involved, including the formulation of a vaccine/drug, dose, route, and frequency of administration, host genotype, host health condition, etc. The detailed mechanisms of the biological processes induced by the administration of a large number of vaccines and drugs are still largely unclear.

Biomedical ontologies are sets of terms that represent entities in the biomedical world and how they relate to each other. To support automated reasoning, the ontology terms are associated with documentation and definitions and organized with logically defined relations using a formal ontology language. Ontologies have dramatically changed how biomedical research is conducted. The Gene Ontology (GO) is a well-known example of an ontology created for the primary purpose of providing controlled and standardized terms for naming different types of biological processes, cellular components, and molecular functions. GO allows the common representation of attributes of gene products regardless of species of origin. Creating such ontology-based annotations is highly valuable for both querying databases and analyzing high throughput data. Since GO was first published in 2000, GO has been widely used, as demonstrated by over 2,000 peer-reviewed publications citing GO in PubMed, and approximately 30,000 documents citing GO in Google Scholar.

So, do we have biomedical ontologies in the vaccine and drug areas, and if yes, how do they help vaccine and drug research, development, and clinical support? Over the last few decades, many vaccine and drug-related terminology systems and ontologies have been developed and have extensive usage. For example, the controlled terminology systems National Drug File – Reference Terminology (NDF-RT), ReNorm, Medical Dictionary for Regulatory Activities (MedDRA), and Systematized Nomenclature of Medicine (SNOMED) have been commonly used to represent drugs, vaccines, and various adverse events associated with vaccine/drug uses. The recently generated Vaccine Ontology (VO) has been used to ontologically represent vaccines, vaccine formulations, and vaccine-induced immune responses. The Ontology of Adverse Events (OAE) and Adverse Event Reporting Ontology (AERO) have been used for representing and reporting various aspects of adverse events. These systems have been widely used in clinical and research settings.

To provide a platform for scientists to demonstrate research progresses, share ideas, address questions, and promote collaborations for better representation and analysis of vaccine and drug-related terminologies and clinical research and data, the workshop “Vaccine and Drug Ontology Study of the Mechanism and Effect” (VDOSME) was organized and held July 21, 2012, in Graz, Germany. This workshop was part of the third International Conference on Biomedical Ontology (ICBO 2012). Detailed information about VDOSME 2012 is available online. In this workshop, six full-length papers plus one short paper were orally presented. Many topics, including the relationship between drug and vaccine ontology informatics, updates of adverse event-related ontologies, and future challenges and opportunities, were discussed. The workshop attendees all agreed that such a workshop was very beneficial to community-based vaccine and drug-related ontology development and applications. The six full-length papers were invited for extension and accepted for publication in a thematic series in Journal of Biomedical Semantics (JBMS).

Yongqun He is Director of the He Group, which conducts dry-lab bioinformatics research and wet-lab Brucella microbiology and immunology research. He is also an Associate Professor in the Unit for Laboratory Animal Medicine (ULAM) and Department of Microbiology and Immunology at the University of Michigan

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