© The Royal Society of Chemistry 2016. The complexity of engineered nanomaterials with regard to their structure and system-dependent properties, and limits of instrumentation to fully characterize nanomaterials in aqueous suspensions or biological media make it difficult to understand how material structure invokes biological response. In this work, a data visualization tool was developed to explore the results of 151 zebrafish assays stored in the Nanomaterial-Biological Interactions Knowledgebase. Visualizations generated using the tool indicated that some nanomaterials exhibited a tendency to cause death, others, sublethal abnormalities. The visualizations also showed that combinations of characteristics, such as the material of the core, shell, and surface, more than any individual characteristic, influenced toxicity. Notably, the size of the nanoparticle did not appear significant in determining toxicity across studies. There was an indication that surface charge could affect toxicity, but a distinct relationship between charge and biological response was not identified. Through exploration of the Knowledgebase using the tool, it was determined that it is possible to alter the toxicity of a nanomaterial of a certain core composition by adding different combinations of a shell and/or a functional outer surface, suggesting that proper design choices, as required to achieve a specific function of a material, could mitigate or exacerbate toxicity.