Taking notes with Scrivener? DevonThink? Notebook? Zotero?

I’m a grad student in the sciences. What I really really am looking for is a program that lets me:

  1. view a PDF (or other file) either in the program or in a separate window, and take notes on it
  2. the notes should be linked to the PDF, and it would be great, but not essential, if they could be linked to a specific section of text in that PDF
  3. I’d like to enter multiple notes from one PDF just by hitting return or tab or something between notes. Ie “factoid 1” return “factoid 2” return - and each factoid appears on its own card and linked to the original file [Alternate scenario - I enter the key reference info once at the beginning, and all subsequent notes keep the same reference info until I change it]
  4. The notes should be able to be tagged with topics
  5. I want to visually (like Scrivener’s corkboard) be able to rearrange my notes, put them in folders, tag them, use the same note in multiple folders, order them.

So far, I’ve tried several programs. Here’s my pros and cons of each:

Skim - great for reading and minor annotations, but doesn’t let you quickly add multiple notes one after another (you have to work with multiple floating windows or in-place notes that cover the text) and doesn’t export to Scrivener in a friendly way - you get one long text file, not a ton of index cards that link to the original PDF.

Zotero - LOVE it for reference managing, but can’t find the love in the note taking abilities. While the notes do stay associated with their file, you can’t seem to arrange them for writing in your own order, you can’t mix and match notes from different references, and you have to click several times to get a new note - not easy for rapid note taking.

Evernote - love it for managing clips and tagging, but again you can’t rearrange them in space nor get into Scrivener easily

DevonThink sounds interesting, but it’s not intuitive, and I admit I haven’t invested the necessary time to figure out its features. I’ll work harder at it if it does what I want.

Scrivener itself - not bad, can use keyboard shortcuts to quickly make new notecards and move around, but pasting a reference into each and every card is a pain. Without a batch paste (where I could take multiple notes, then select all those cards and paste a reference into the notes or title or something), it’s a pain. I might take 100+ notes from a reference and manually opening each one and pasting in a reference is a pain.

Does anyone have any suggestions or things I’m missing?


Depending on the content of the PDF file - really this is only good for PDFs that are mainly text - you can use Scrivener’s Documents > Convert > PDF File to Text to convert the PDF files to text and chop them up. So, you could:

  1. Use cmd-D to duplicate the PDF (so that you keep the original in the project for reference).
  2. On the copy, go to Documents > Convert > PDF File to Text.
  3. Drag the PDF file into the references pane of the inspector for the text version of the file, so that you can easily access it.
  4. Set up the split view so that the PDF file is open in one view and the text version open in the other.
  5. Use cmd-K (Documents > Split at Selection) to start cutting up the text version into smaller chunks (the newly created documents will have the same references as the original).
  6. You can use the “Auto-Generate Synopsis” button in the inspector (top-right of the index card) to automatically generate the index card text for each split up document (if there is no selection, the first few sentences will be used, otherwise the selected text will be used).
  7. You could drag all of the text document chunks into the references pane of the PDF document, so that you can access them from there, too.

At this point, you have the PDF document open in one pane, and access to lots of other documents with just sections from the PDF document. You can make notes on all the different sections in the text version, cutting out or keeping what you need, but always having reference to the PDF original.

This is only one way of doing it, of course; it doesn’t do exactly what you asked, but it is a decent way of making notes on a PDF file, I think.

Hope that helps.

All the best,

Keith, thanks for that! I’ve copied and filed it away in my Scrivener notes. :smiley:

The problem is that you can’t export the notes and combine them…or can you?

Yes, you can, using File > Compile Draft and selecting to include the notes.
All the best,
P.S. I received your e-mail and will reply properly tomorrow (I’m in the UK so it’s Sunday evening here).

Thanks, Keith. I’ll look forward to your email.