Computer-program products and methods for automatically annotating terms, such as ambiguous terms, in an electronic text document are disclosed. In one embodiment, a method of annotating a text document includes determining, by a computing device, a term of interest within the text document. The method further includes searching a data structure including incongruous term pairs (tx, tt) determined from a controlled vocabulary for the term of interest appearing as a term tt, wherein the term tt is a linguistic head of a term tx of the incongruous term pairs (tx, tt). The method further includes annotating the term of interest with a meaning provided by the controlled vocabulary only if a term tx of the incongruous term pairs (tx, tt) associated with the term of interest in the data structure is not present within a predetermined textual distance of the term of interest in the text document.