15. The method of claim 9 , the marked-up document being provided by the computer processor as a single data stream.
9. A computer-implemented method of annotating a shared document, the method being executed on a computer and comprising: responsive to a request from a user to retrieve a shared document, retrieving, in a computer processor, the shared document from a document data storage as document data; inputting, in the computer in response to the user, at least one annotation to be applied to said shared document in association with a section-dependent, display-independent location; inputting, in the computer processor in response to the user, a section of the document data to be associated with the at least one annotation; providing , in the computer processor, the shared document as a marked-up document for display at a user interface, the at least one annotation being visually reproduced in association with the section of the shared document, the shared document having plural sections each having a user-selectable length, the plural sections including the section of the share document within which the annotation data is to be embedded, wherein the at least one annotation includes, specific to the section of said shared document to which the at least one annotation is applied, a pre-defined conflict indication which is user-selected from at least two of the following: yes, possible and/or no; revising, in the computer processor in response to the user, the at least one annotation from the marked-up document displayed at the user interface, and a scope of the section of said shared document to which the at least one annotation is applied; and responsive to a request from the user to store the shared document, extracting, from the marked-up document, the annotation data and the scope of the section of said shared document to which the at least one annotation is applied, updating, in the annotation data storage, from the annotation data that was extracted, the at least one annotation and the scope of the section of said shared document to which the at least one annotation is applied, and storing, in the annotation data storage for later retrieval, the at least one annotation and the scope of the annotation data that are revised.