This paper presents an ontological approach of scientific experimental data integration across complementary sub-domains, i.e., agricultural production and food processing, with an application to viticulture and winemaking. The two main steps in this approach are (i) to integrate preexisting ontologies to create a so-called ontology network and (ii) to populate the ontology network with experimental data from various sources. The Agri-Food Experiment Ontology (AFEO), a new ontology network, was developed, based on two ontological resources, i.e., AEO (Ontology for Agricultural Experiments) and OFPE (Ontology for Food Processing Experiments). It contains 136 concepts which cover various viticulture practices, as well as winemaking products and operations. AFEO was used to guide the data integration of two different data sources, i.e., viticulture experimental data stored in a relational database, and winemaking experimental data stored in Microsoft Excel files. Two applications illustrate the approach. The first one is on wine traceability and the second one is related to the influence of irrigation practices and winemaking methods on GSH concentration in wine. These examples show that data integration guided by an ontology network can provide researchers with the information necessary to address extended research questions.