With the increase of the world population, waste production and its impact on the environment increase. Wastes can be an opportunity for the development of a circular economy and an industrial ecology. This paper proposes a framework based on KE, sustainability engineering and life cycle thinking for supporting decisions on agricultural by-product valorization dedicated to engineers, academics, managers and policy decision makers. Five steps describe the framework: the definition of the goal and the scope, the extraction of the relevant information from heterogeneous data source feeding ontologies, the life cycle inventory, the impact calculation assessment and the results ranking. A case study related to agricultural by-product valorization, in the biorefinery area, allows to validate the approach and the associated framework. Rice straw is transformed in glucose for bio-carburant production. Four different rice straw pretreatment processes are analyzed using a collection of data sources. The framework calculates sustainability indicators and allows to ranking the four technologies of case study supply chain.