Methods, systems, and apparatus, including computer programs encoded on computer storage media, for disambiguating join paths for natural language queries. One of the methods includes, obtaining a natural language query from a user; parsing the natural language query into structured operations to be performed on APIs of a knowledge base, including: responsive to detecting a parsing ambiguity in which the natural language query can be parsed in two or more ways: providing, through a user interface, to the user one or more information items identifying the parsing ambiguity; responsive to a user interaction with an information item: modifying the parsing in accordance with the user interaction to generate one or more structured operations; performing the one or more structured operations on the structured APIs of the knowledge base to determine one or more search results; and providing one or more search results to the user.