Nowadays, customers require customized products instead of standard offers and in many cases prefer web shops and market places for purchasing goods and services. Therefore, intelligent product configuration tools are great value for many companies. One of the main components of these tools is a configuration model. In order to integrate the configuration model to the semantic web new approaches to the representation of product configuration knowledge are needed. In this paper, we present a layered ontology modelling framework for building semantic product configuration models and provide the corresponding methodological approach to product configuration. The approach enables building distributed product configurators that use semantic configuration models in the form of web ontologies and Shapes Constraint Language (SHACL) to validate integrity constraints of individual configurations. SHACL is also used to query the model and to represent additional constraints required by different applications. The provided method is demonstrated on the basis of the real case study from timber industry that specifically covers thermally modified timber (sawn wood) products.