Racz, R. | bioRxiv Science

bioRxiv2025

VO: The Vaccine Ontology

With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly, we have since 2007 developed the community-based Vaccine Ontology (VO), which aligns with the Basic Formal Ontology and adheres to OBO Foundry principles. VO models ontologically vaccines, vaccine components, vaccine immune responses, vaccine investigation studies and other vaccine-related topics. VO represents more than 10,000 vaccines targeting 289 infectious pathogens and cancers in humans and over 30 nonhuman animal species. VO provides mappings to external resources such as RxNorm, CVX, FDA, and USDA. Various VO use cases exist. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). Semantic queries can be made to query VO. VO has been shown to enhance experimental and clinical vaccine data analysis and vaccine literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era.

bioinformatics↗

bioRxiv2025

predicTox: An integrated database of clinical risk frequencies and human gene expression signatures for cardiotoxic drugs

We have used drug-induced transcriptomic responses and whole-genome sequences in healthy human induced pluripotent stem cells (iPSC)-derived cardiomyocyte lines to identify cellular functional pathways and genomic variants potentially associated with the cardiotoxic effects of tyrosine kinase inhibitors (TKIs) and other cancer drugs. Here, we describe predicTox.org, an interactive website that organizes our data and its integration with knowledge from cell pathways and genomic databases. DrugTox summary cards give results of these analyses and metadata for each drug. Fields include FDA Adverse Event Reporting System (FAERS) cardiotoxicity risk scores, cell pathways, and genomic variants potentially associated with drug-induced cardiotoxicity. At a detailed level, predicTox provides ranked lists of pathway signatures that are common for cardiotoxic TKIs, up- and downregulated pathways associated with cardiotoxicity induced by specific TKIs and TKI-regulated genes mapping to those pathways. predicTox provides downloadable lists of drug-induced differentially expressed genes (DEGs) and pathways, drug-related genomic variants associated with cardiotoxicity, all with their statistical metrics, and mathematical models to simulate drug effects on heart physiology. Building on the results of our algorithm for independent reidentification of the well-known rs2229774 variant for anthracycline-induced cardiotoxicity, we describe how our data can be queried to identify potential variants associated with drug-induced cardiotoxicity by affecting a drugs pharmacodynamics and pharmacokinetics.

cancer biology↗