The FISA court system, the proceedings of which are closed to the public and the records of which are classified, is "transparent," President Obama told Charlie Rose in an interview broadcast on PBS last night:
It is transparent. That's why we set up the FISA court. Look, the whole point of my concern, before I was president—because some people say, 'Well, you know, Obama was this raving liberal before. Now he's, you know, Dick Cheney.' Dick Cheney sometimes says, 'Yeah, you know? He took it all lock, stock, and barrel.'
My concern has always been not that we shouldn't do intelligence gathering to prevent terrorism, but rather are we setting up a system of checks and balances? So, on this telephone program, you've got a federal court with independent federal judges overseeing the entire program. And you've got Congress overseeing the program, not just the intelligence committee and not just the judiciary committee—but all of Congress had available to it before the last reauthorization exactly how this program works.
"Transparent" in this case seems to mean "overseen in some way by all three branches of the federal government." Which is something, certainly, even if FISA warrant requests are almost never denied by the courts, but I'm not sure it counts as "transparent."
Obama and Rose also discussed Syria, which the president correctly noted "is not Iraq."