All varieties are defined over $\mathbb{C}$. Let $\pi : X \to C$ be an elliptic surface with $X$ and $C$ smooth. Then there is a Jacobian surface $\overline{\pi}: J(X) \to C$ (with a section) associated to $X$. Do we also have a morphism $\varphi : X \to J(X)$ such that $\overline{\pi}\circ \varphi = \pi$? (If yes, a precise reference for the construction of that morphism would be greatly appreciated!)

I think the following at least gives a rational map: Choose a curve $D$ in $X$ which maps dominantly to $C$ with degree $n$. For a smooth fibre $F$ of $\pi$ define a map to the correspoding fibre of $\bar{\pi}$ by sending a point $p$ to the class of $n[p]  [F\cdot D]$. (This is a cycle of degree 0.) With a little work one can check that this gives a well defined rational map which is a morphism over the smooth locus. It seems unlikely though that the above actually gives a morphism in general. 

