Linking Scrivener with large collection of research pdfs

Hi. I’m engaged in a non-fiction project which requires downloading a lot of research, mostly pdfs, and grouping them/storing them in a way that I can find material easily, classify them, comment them, and then relate them to my Scrivener manuscript.

At the moment I put my pdfs in Windows folders and sort by subject. Within the subject folder, I group by author name. This whole procedure is not very satisfactory.

One alternative would be to use Google Sites, which I have found useful for my company’s ‘How to’ institutional memory. I would structure my new project in Google Sites by alternating normal pages with filing cabinet pages. The ‘normals’ would contain the overall structure and notes. The filing cabinet pages would contain the downloaded research pdfs.

This will be clunky. Working this way means duplicating my existing Scrivener structure in another application. But since Scrivener does not allow storing and linking to pdfs, I see no alternative. How do others deal with linking to their research databases? This must be a very common problem.

I use Papers 3 from Mekentosj for exactly what you are describing: downloading, grouping (in collections), annotating and then copy a complete “note” into Scrivener*, consisting of the reference, my annotations, a link back to the Papers 3 collection, and a citekey that can be used in the Scrivener text to get a correct reference list.

*) In reality I go via Scapple, where I arrange the general outline of the paper I am writing, before importing into Scrivener.

On first view, Papers 3 seems a little primitive, is that right? I downloaded it and the following happened:

  • It tried to import my Dropbox papers. When that failed, no prompt for a different password appeared, and it is not clear how to get it to do this
  • The menu is blue on blue, so invisible on my laptop
  • Papers 3 doesn’t seem to integrate into Windows. Instead it sits on top of the screen, so it is hard to close (no typical Window ‘X’ to close the application) and I couldn’t find any way of adjusting its size (some of the menu items are off-screen).

Usually when I meet software at this stage of development, I give it a miss.

A large list of grumbles about Papers3 from a distinguished set of academics: … ppointing/
Excellent comparison of other systems: … t_software
Some comments here: … -software/
I also found this useful: … e_managers

I run the Mac version, not Windows, and I have read the grumble but don’t agree. And I am not convinced about how “distinguished” the grumblers are, myself being an academic. :wink:

My menu is not blue, it’s grey, and importing pdf’s was very simple. You just specify the folder where you have the pdf’s.

But, if you don’t like it, don’t use it. You won’t be very productive using software you don’t like. I like it, so I use it.

Reference Management Software is a large category of which I was previously unaware. I see many do similar things, viz Mendeley, Zotero, Paperpile, Quigga, and Readcube. The interfaces are almost identical, as are the function lists.

Most allow one to comment pdfs, attach notes to individual pdfs, but do not put one’s own notes at the core of the navigation. I was looking for something in which my notes would be more centre-stage, connecting the references. Docear seems oriented in this direction.

But Docear encourages one to use it as one’s principal writing tool. No, no - I want to use Scrivener. But I want a Scrivener (a) with powerful reference management capacities, allowing one to source, add and classify external pdfs as easily as say, Mendeley; (b) with mind-mapping capacity. The cork board is half-way there, but maybe an extra widget next to it with Docear’s mind-mapping tools (which I believe are actually some other software) would be nice?

(Revision: just looked up Scapple. Wow! Amazing!
Note to self: quit commenting before you’ve done your research)

I’ll have to experiment with Scapple. At first glance it seems too static. I would like it more like Google Sites (a) with ability to tab pages, so that you are not just stuck with one page on which you place notes (b) the ability to hyperlink notes on one page to another, so that you can create a really deep universe of notes.

Hmmm… A deep universe of notes? Isn’t there a big risk that you (metaphorically) will get lost in a universe and never find your way back to where you started?

Scapple is very simple, but at the same time extremely flexible. I copy all my annotations from Papers3, using an Apple script provided by Mekentosj, so I get exactly the information I want, including a link back to the pdf in Papers. Then I can shuffle things around in Scapple, make the connections I want, add comments, etc, and finally import my “outline” to Scrivener.

My experience, after a long time doing science, is that you need to keep all important facts in your head, not on paper or on a computer, or you won’t ever be able to come up with a really new idea. You need to read a lot, think a lot, make annotations, draw conclusions, and put things together in your own mind. A “deep universe of notes” won’t help you doing this. A database with pdfs will help you find that special article you have a vague memory you found something special in, and a “mind-map” in Scapple or some similar software will help you organize your thoughts. But in the end it all comes down to doing some hard thinking.

Docear’s mind mapping is built on Freeplane. You can get Freeplane separately if you don’t need the rest of Docear. Freeplane itself is based on Freemind. Both use a .mm format for their mindmaps. Scrivener can both import and export to this format. Whether that helps you out, well, you’d have to play around and see.

One note - be careful with Docear. I presume they’ve fixed it by now, but earlier in the summer there was a bug in their installer which could do unfortunate things to your computer. The zip download was supposed to be fine however.

I am not a scientist but more of a historian, and we work differently. That’s why I asked the question originally. After all this talk, frankly, I am a bit surprised to be told that I shouldn’t want to work the way that I made clear that I did want to work. A flat pdf search facility is one part of the solution, but on its own, of minimal use to me… I already have that on my PC anyway, since I still use the excellent Google Desktop search facility.

Depth is the way to go. I have experience of managing a team of people supporting a large complex property research website through Google Sites. I could never remember how to do everything, nor could my staff, but Google Sites remembers for us. It is wonderful!

It is just the same with my history work. I need to be able to store large quantities of my own thoughts strategically linked to different pdfs. It is NOT about finding that vital single paper… it is about organizing a story.

There is absolutely no danger of getting lost, due to the Google Sites’ tabs. In our Google Sites company ‘institutional memory’ site, everything is grouped under 9 top-level tabs, which leads to a deep set of “How to” pages, which are richly interlinked via hyperlinks. There is also a good search. If we have something new we want to document, we just put in on the appropriate section and link to it. It takes five minutes and it is very easy. I suppose we could order all staff to remember everything, but what would be the point? It would stress them and me out, and when they left, we would have lost the knowledge.

So for Scrivener I would suggest an extra widget next to the Cork Board, integrating Freeplane (the mind mapper Docear uses which supports hyperlinks) with Google Sites, which supports tabbing. Just an optional extra.

Those that don’t like it, don’t need to use it!

I thought I had found my solution. It is not integrated with Scrivener, but what can you do (I assume that Zotero will eventually be integrated). It is Microsoft’s OneNote, and thanks for the suggestion to . For Mac users, he suggests Circus Ponies Notebook and DEVONthink. His comments about Scrivener are spot-on, so I trust what he says.

However OneNote is not ideal, as there’s no way of linking to a local folder containing pdfs. Clearly, one wants to be able to link to pdf collections, as well as individual pdfs. Linking to pdf folders is possible via DropBox (via the remote interface), but then to open the pdfs you need to download them…roundabout!

I’m a bit late to the party, but you should consider using Sente – by far the most powerful biblio-software PLUS, especially pertinent in your case, the best notes/annotations I’ve ever seen. There’s a Butler Library (Columbia) series of blog posts which discuss how to use it most efficiently. There’s a moderate learning curve, as there is to Advanced Scrivener, but it’s worth it. If you want a PDF storage container – a place just to keep thousands of PDFs that you can search through instantly for phrase, tag, etc., use Evernote Premium. For the time being, I’d keep away from DevonThink. I used it for years happily but its syncing is a debacle. Nothing but bugs for the last six months and support is very patchy. I just dragged over six databases into Evernote and it syncs/works like a charm. [P.S.: I’m an historian, too, so I’m confronted by some of the problems as you, I imagine.]

The OP is on Windows! No Sente or Bookends, which are Mac only … at least Bookends is.

Mr X