Let $X=\operatorname{Spec}(R)$ be an integral scheme with generic point $\eta$ and let $Y$ be a separated scheme.
A rational map $X\leadsto Y$ is a certain equivalence class and it is represented by an actual morphism of schemes $U\to Y$ where $U$ is a dense open subscheme of $X$. I chose the above properties for $X$ and $Y$ since two morphisms of schemes from a reduced scheme to a separated scheme which agree on a dense open subscheme of the domain are the same.
Since $\operatorname{Spec}(\mathcal{O}_{X,\eta})$ is the inverse limit over all the open subschemes $U$ of $X$, every rational map $X\leadsto Y$ should define an actual morphism $\operatorname{Spec}(\mathcal{O}_{X,\eta})\to Y$ of schemes.
Is the data of a rational map $X\leadsto Y$ the same as an actual morphism $$\operatorname{Spec}(\mathcal{O}_{X,\eta})\to Y$$ of schemes?
I think that this is not true (see the example in the comments by Zhen Lin): Every element $f\in \operatorname{Spec}(\mathcal{O}_{X,\eta})$ comes from an dense open subscheme $U$ of $X$ but there is probably no common $U$ for all such elements.
Then, a rational map $X\leadsto Y$ may perhaps be seen as a generalization of a scheme morphism $X\to Y$ but it is more special than a scheme morphism $\operatorname{Spec}(\mathcal{O}_{X,\eta})\to Y$. Is this intuition correct?
In that case, I wonder about this question:
Is there a scheme $Z$ together with scheme morphisms $\operatorname{Spec}(\mathcal{O}_{X,\eta})\to Z\to X$ such that a rational map $X\leadsto Y$ can be defined as an actual scheme morphism from $Z$ to $Y$?