Knowledge of the composition of the Earth's interior is highly relevant to many geophysical and geochemical problems. Neutrino oscillations are modified in a non-trivial way by the matter effects and can provide valuable and unique information not only on the density but also on the chemical and isotopic composition of the deep regions of the planet. In this paper, we re-examine the possibility of performing an oscillation tomography of the Earth with atmospheric neutrinos and antineutrinos to obtain information on the composition and density of the outer core and the mantle, complementary to that obtained by geophysical methods. Particular attention is paid to the D$^{\prime \prime}$ layer just above the core-mantle boundary and to the wat...