Knowledge in pharmacogenomics (PGx) is scattered across several resources, e.g., reference databases and the biomedical literature. Matching their content would thus lead to a consolidated view of the available PGx knowledge that could, in turn, support multiple downstream applications, including knowledge curation and precision medicine. However, matching atomic units of PGx knowledge is challenging due to their peculiarities: they are of n-ary nature, represented with heterogeneous vocabularies, and with various levels of granularity. In this paper, we frame the matching of PGx knowledge units of various provenance as an instance matching problem. We summarize our work to represent such units within a knowledge graph named PGxLOD, and to match them with a rule-based and a graph embedding-based matching approaches. We then particularly discuss the remaining challenges and how our research artifacts opened to the community could foster new benchmarks and methods for structure-based instance matching.