If you start with a logical query $p(X) \lor q(Y)$, this would correspond to a Prolog-style "goal clause":
:- p(X) ; q(Y).
From the standpoint of SLD resolution on Horn clauses, the above query can be interpreted as a logical proposition implying a contradiction or falsehood:
$$ (p(X) \lor q(Y)) \to \textit{false} $$
Reaching the contradiction corresponds in the Prolog programming to success of a goal clause/query.
Now in the context of Prolog programming it does not make sense to identify the single goal clause above to a pair of goal clauses:
:- p(X).
:- q(Y).
It is unclear what exactly you mean by this identification, since there can be only one goal at a time for the Prolog engine to pursue. Although resolution of one goal may lead to attempting subgoals, these are pursued serially.
On the other hand the goal clause:
:- p(X), q(Y).
would ask the Prolog engine to first attempt to satisfy p(X) and if successful, then to attempt to satisfy q(Y) (with the possibility of backtracking into the first goal p(X) if any choice-points are left open when it fails in trying q(Y)).
So the latter goal clause corresponds to the logical query $p(X) \land q(Y)$, not $p(X) \lor q(Y)$.
:- p(X) | q(Y). – hardmath Feb 23 '16 at 14:45