New challenges in agronomic research aim to understand interactions between molecular elements responsible of the phenome. These interactions are complex to decipher because they are expressed at different molecular scales and are strongly influenced by environmental factors. Recent advances in high-throughput technologies only partially capture these dynamics. We have developed AgroLD, a knowledge graph that exploits the Semantic Web technology and some of the relevant standard domain ontologies, to integrate information on plant species and in this way facilitating the formulation of new scientific hypotheses. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics.