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The paper presents an interdisciplinary project which is a work in progress towards a 3D Geographical Information System (GIS) dedicated to Cultural Heritage with a specific focus application on the Castle of Shawbak, also known as the “Crac de Montréal”, one of the best preserved rural medieval settlements in the entire Middle East. The Shawbak archaeological project is a specific and integrated project between medieval archaeological research and computer vision done thanks to a long cooperation between University of Florence and CNRS. Focusing mainly on stratigraphical analysis of upstanding structures we provide archaeologists a two-step pipeline. First a survey process using photogrammetry, both in a traditional way and using the most advanced technique for obtained dense map and then a tool for statistical analysis. The photogrammetric survey is driven by an archaeological knowledge which is formalized by ontologies as a link between all the archaeological concepts which are surveyed. The archaeological knowledge studied is now limited to stratigraphy of upstanding structure using a stone by stone survey as well as a 3D reprojection of archaeologist design made on photographs. The 3D GIS is the last step of this chain and aims the automatic production of 3D models through archaeological database queries: these 3D models are in fact a graphical image of the database and at the same time the interface through which the user is able to modify it and produce different kind of analyzing. All these developments are written in Java within ARPENTEUR framework. [ABSTRACT FROM PUBLISHER]