This paper proposes a control-oriented modeling and identification framework for flexible-joint robot arms using motor-side measurements only. From the perspective of model-based control strategies including an inner feedback linearization loop, the proposed method allows an explicit treatment of the vibrational behavior induced by the flexibilities. A theoretical model of the partially decoupled system is derived and a frequency-domain identification procedure allowing an estimation of the flexible parameters is detailed. The obtained description of the system is experimentally validated on the CEA lightweight robot arm ASSIST.