Papers notes & DTPO

This is my first post on the forums, so apologies if this topic has already been covered.
I am a doctoral student using Papers, Bookends, DTPO and Nisus Writer in my workflow. I like the way I can find journal articles in Papers and then read through them full screen and make notes in a window that overlays the full screen mode. This makes reading and synthesising the article easy. However, when I sync my Papers folder with DTPO, the notes I have taken are missing (or at least I can’t find them). Has anyone come across a similar issues using Papers and DTPO in this way. If so are there any workarounds or things that I have missed, that I should be doing.
Any assistance would be greatfully received.

Auckland, New Zealand.

Hi Dave

I have a similar system set up using DTPO to catalogue journal articles and Skim to read them and make notes. When I open the paper with Skim I can see my notes but DTPO only shows the unmodified PDF file. When you say that you can’t see your notes is that because you are opening the file in DTPO? If you open it again in Papers are your notes still there?


DEVONthink doesn’t alter the indexed (or imported) PDF, so his notes should be visible in Papers.

I don’t use Skim, for the simple reason that it limits notes and annotations to PDFs only. But I’ve got many file types in my collections of references and notes, and I want to be able to make comments or annotations concerning documents regardless of the file type.

I’ve evolved several ways of doing this, involving hyperlinks, Comment information and/or Sheets. I can easily link a note to a document to which it refers. If I end up with a collection of notes about a large document, it may become useful to create a Sheet that lists all the notes that refer to a certain document, perhaps specifying relevant page numbers to which notes refer. Although one cannot link from a Record (or Sheet), if the Record (or Sheet) contains the Name of a note, I select that Name and do a Lookup (Command-/) to immediately bring it up.

I think the largest number of such notes “attached” to a single document that I’ve done ran to over 30 notes. I found this a “rich” way of working, because those notes could also contain information and links relating to other documents as well (networking ideas and sources), Some of the notes evolved into drafts of portions of the final product, or into footnotes. All such notes are searchable, and immediately available for cut/paste in assembling the final product, with few or no format editing problems.

Thanks for the helpful advice. I will certainly look in more detail at just what DTPO can do regarding making notes about references i.e. Sheets. The only reason I wanted to be able to make notes in Papers that I could then store and search in DTPO is that Papers seems to do it better from a UI perspective. I like being able to have the pdf open and to be able to make notes on a transparent ‘notes window’ as I read the file. Not sure if the DTPO full screen mode allows this.

I think as my knowledge and understanding of DTPO grows so will the extent to which it becomes the core of PhD work.