A digital publishing platform enables users to create and organize notes associated with electronic, published documents. Sets of notes, each associated with a document, are uploaded to the publishing platform by notepad applications executing on user devices. Each set of notes has one or more notes, and each note includes a link to a location in the associated document. The publishing platform is configured to aggregate a plurality of sets of notes, combining the notes of the sets into a single set while maintaining their link to an associated document.