1. A document processing system comprising: a storage unit that stores a plurality of items of document data and relation information representing relations between the plurality of items of document data; an input unit that inputs document data; a specifying unit that specifies document data related to the document data input by the input unit among the plurality of items of document data stored in the storage unit; and a control unit that controls to store estimated relation information which is different from the relation information, as information representing a relation between the document data input by the input unit and the related document data specified by the specifying unit.