In order to correctly assess the nutritional quality of a meal or a manufactured food product in a given country, the first step is to assess the nutritional values for its ingredients. Food composition databases (FCDBs) available in a lot of countries and managed at national level provide values for energy and nutrients of food components. Unfortunately, values associated with some nutrients of interest may be lacking in the FCDB of the country in which the nutritional quality must be assessed. Finding values associated with nutrients for similar foods in other FCDBs is a way to deal with incompleteness. An additional issue arises because the vocabulary used to describe the ingredients of a meal or a recipe in a given FCDB is usually different from the one used in other ones. In this paper we address the problem of identifying the nutritional value of recipe's ingredients by querying different FCDBs through FoodOn as pivot ontology. We present a new alignment method between two distinct FCDBs, based on syntactic and semantic approaches, whose vocabulary is previously transformed into an ontology. Our method has been evaluated on Ciqual, the French food nutritional database, USDA, the United States food nutritional database and the FoodOn ontology. The incompleteness management task based on FoodOn as pivot ontology has been assessed with a real use-case concerning iron, Vitamin B12, Vitamin C nutrients.