Our group purchased the code a "EMR" program that was a flat file database in access.
We contracted with a company to make make the database relational (SQL) and to add a few features. We now have our contractor that says the database/program is ready to go, but our IT department says it has not been validated. I am an MD with minimal database experience. What questions should I be asking. I do no want to throw our new product away, but I also can't use it if it is not structurally sound.

Thanks,
Mark

Only your IT department can tell you what their standards are for software acceptance.

Your project ought to include a test strategy to verify that the software is fit for purpose and does what the contractor is being paid for. The IT Department will probably want to see evidence of what testing was done and probably do additional testing for themselves as well. Among other things there ought to be some validation to ensure that the data has been transferred correctly from the old system to the new.

I've worked on patient databases at healthcare institutions myself. I find it almost scandalous that patient medical records would ever be held in an Access database. No criticism intended of you but perhaps your IT Department are at fault for allowing such a state of affairs to exist in the first place.

Can our IT department do the tests? Does it have to be the vendor? The vendor says it is ready to go and it has referential integrity. I have tried the program a few times and it seems like it is OK, but I want assurances. If the vendor won't do further testing can our IT or some other company do the tests. Can the tests be automated?

I suggest you ask your IT department. Yes in principle anyone can do the tests. Yes the actual execution of the tests can be automated once the tests have been created.