When I had my house built, I had the contractor rough in plumbing for a basement bathroom. I have a bi-level house so when I was going to install the toilet I noticed that there was a pipe hanging out of the basement ceiling above where the toilet is going. Since the piping was already installed and under the concrete floor does this mean I am going to have to dig the floor up to connect the vent to the toilet drain or is there another vent hooked up some where else on the drain line

This will depend upoon where you live and the code you fall under, Do you live on the West Coast? UPC mandates that each fixture be vented so if you fall under OPC Code then that just might be the vent for the toilet. What size is the pipe hanging out of the ceiling? On the other hand this could very well be the lavatory vent and if you live in the other 980% of the country your toilet may already be wet vented.
Let me show you a typical, (in my area) bathroom group rough in. This configuration only uses one vent for the entire group.
4" ,(under cement and basements) 3" (on first and second floor) from the toilet to the main. The lavatory to connect to the toilet drain line and vent to the roof or revent back in the attic to a existing roof vent. The tub/shower to connect to the lavatory drain line and be wet vented by it as will the toilet. Be advised to always check local codes before changing or remodeling your drainage system.
As I said, It all depends on where you liive and the code you fall under Good luck, Tom