1. A method for annotating a markup language document with a visual representation of ink (a digital ink annotation) and storing said digital ink annotation, comprising the steps of: acquiring digital ink by capturing input from a user who is annotating a markup language document; rendering the digital ink and the markup language document in a browser window, wherein said rendered digital ink forms a digital ink annotation of said markup language document; associating at least one element in the markup language document with the digital ink annotation; and storing the digital ink annotation wherein the associated at least one element acts as an anchor in the markup language document for the digital ink annotation.