We present an interactive modeling tool, VERA, that scaffolds the acquisition of domain knowledge involved in conceptual modeling and agent-based simulations. We describe the knowledge engineering process of contextualizing large-scale domain knowledge. Specifically, we use the ontology of biotic interactions in Global Biotic Interactions, and the trait data of species in Encyclopedia of Life to facilitate the model construction. Learners can use VERA to construct qualitative conceptual models of ecological phenomena, run them as quantitative simulations, and review their predictions.