Clinical and epidemiological researchers across all medical specialties need tools and knowledge representations to support the classification, aggregation, and analysis of medication data. The Veterans Affairs National Drug File Reference Terminology (NDF-RT) is a named standard for classifying medications. We describe our experience applying NDF-RT to aggregate RxNorm-encoded medications that were collected from an international cohort of over 8,000 children. We detail the researchers' analysis objectives and subsequent requirements for a drug classification representation, and assess the ability of NDF-RT to provide classes that are meaningful to pediatric researchers. In addition, we explore the completeness of RxNorm - NDF-RT mappings (i.e., the coverage of NDF-RT) for this sample of pediatric medications. We conclude that NDF-RT is sufficient to address the knowledge representation needs for this research study, though only a small subset of NDF-RT is needed for research analyses. Researchers from all domains would benefit from tools for easily extracting a set of relevant classes from the NDF-RT knowledge structure.