I used to get this ages ago when I ran track and marathons, sometimes oh man it hurt pretty darn bad. I found it bothered me the least when I drank more water and breathed properly. If it got real bad, I would bend over, press on the area and breathe deeply. My coach at the time said lots of runners get it and to make sure to drink plenty of water and stretch before I start... she called it a gas bubble, but I'm pretty sure it's not gas.
If you have concerns that it could be gallstones or something along those lines, get it checked out to ease your mind. You can also stop when you get those pains, do some deep breathing, grab a nice glass of water and get started on some pillates or yoga.