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J Biomed Semantics. 2011 May 17;2 Suppl 2:S8. doi: 10.1186/2041-1480-2-S2-S8.

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.

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  • 1Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.



Interferon-gamma (IFN-γ) is vital in vaccine-induced immune defense against bacterial and viral infections and tumor. Our recent study demonstrated the power of a literature-based discovery method in extraction and comparison of the IFN-γ and vaccine-mediated gene interaction networks. The Vaccine Ontology (VO) contains a hierarchy of vaccine names. It is hypothesized that the application of VO will enhance the prediction of IFN-γ and vaccine-mediated gene interaction network.


In this study, 186 specific vaccine names listed in the Vaccine Ontology (VO) and their semantic relations were used for possible improved retrieval of the IFN-γ and vaccine associated gene interactions. The application of VO allows discovery of 38 more genes and 60 more interactions. Comparison of different layers of IFN-γ networks and the example BCG vaccine-induced subnetwork led to generation of new hypotheses. By analyzing all discovered genes using centrality metrics, 32 genes were ranked high in the VO-based IFN-γ vaccine network using four centrality scores. Furthermore, 28 specific vaccines were found to be associated with these top 32 genes. These specific vaccine-gene associations were further used to generate a network of vaccine-vaccine associations. The BCG and LVS vaccines are found to be the most central vaccines in the vaccine-vaccine association network.


Our results demonstrate that the combined usages of biomedical ontologies and centrality-based literature mining are able to significantly facilitate discovery of gene interaction networks and gene-concept associations.


VO is available at:; and the SVM edit kernel for gene interaction extraction is available at:

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