A typical PLoS article ... the annotation system has not yet revealed itself to me; I see the Annotate function well enough but have not yet discovered a existing annotation so do not know how these are presented. (I've looked at over a dozen papers and have yet to find even a single annotation.) [Found: PLoS ''sandbox'']
see also PLoS explanation and comment guidelines. (Note that "annotation" and "comment" are used interchangably.)
WayBack version of Jack Slocum's explication of his WordPress / EXTJS comment system demonstrates fabulous integration of AJAX functionality. (The original is now 404.) Note that cited text is highlighted when reading comments in place or when commenting on the selected block.
- a historical record of who annotated what, and when
- the ability to display the whole of that record i.e. "all comments"
- indication of where a comment has been placed
- the ability to read a comment in context of its referent, or not
That systems so similar in effect vary so remarkably in detail evidences just how many options there are to be played with.