The convention is that when you first write out the word, you put the abbreviation in parenthesis next to it, so that there is no confusion for the reader. For example, "In summer 2004, I shadowed a gastroenterologist (GI) doing research...." Then you can use GI freely for the rest of the essay (though if you use it a lot, it WOULD be nice if you wrote it out once in a while, it just looks better).