DEVONthink with Zotero Workflow

It’s actually the first request of this kind that I’m aware of. Is anyone else interested in this? What exactly should be exported and how/when/why would this be useful for your workflow? Thanks!


It would be useful to me because (1) RIS is a common denominator of much reference management software; and (2) Tinderbox can input RIS data and incorporate that into its custom metadata, which it terms “Attributes”

That said - @DarylAdair have you experimented with the existing “Create Metadata Overview” feature? Much of what you want to achieve with RIS can already be done with custom metadata exported into a TSV or CSV file via Create Metadata Overview. And much software that exchanges data via RIS can also exchange data via TSV/CSV. So I am not certain that RIS support is needed given the flexibility we already have from that.

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Another point for using Bookends is their incredible support. Whether I write a personal email or post in the forums, Jon would be back with an answer in a matter of couple of hours. Even if he can’t provide a solution right away, he would at least tell you what you can try to achieve what you need.
I don’t know how he can account for 37% of all the posts on Bookends forums, respond personally via emails AND develop Bookends at the same time, this is unbelievable.

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I’m going to chime on two things: first, the idea that DT could scrape/create metadata for a reference manager is BRILLIANT and I want it!, and, second, that Bookends’ Jon is pretty phenomenal in terms of support. (And, kudos for making the file system human readable – I don’t know if Zotero still creates a great galaxy of folders, the way Papers did in its day, but that was just crazy-making.)


Exportable metadata would be very helpful. I use DT as my primary clipping/storage app for various kinds of online sources as well as archival research. In order to organise and reference the resulting documents, I’ve added custom metadata fields.

If I want to cite such materials, I currently need to create manually a record in Zotero. So it would be very useful to be able to turn these fields into .ris files [or similar] which could be loaded into Zotero [or similar].

Hope this makes sense.


that does sound like magic, but I can’t quite see the process. Do you mean you anotate the indexed file in DT? and not quite sure what you mean by ‘links that DT lets you create’. Sorry if I’m being a numpty, but if you could explain it a bit more that would be so good. thanks

I think you meant to reply to @laudunum’s post aobve.

…freaking magical.

The way to do it is not to import your PDFs: leave them wherever Zotero or Bookends places them – Bookends just keeps them in a single directory in the iCloud Drive directory (because I sync with an iOS device) and index them in Devonthink. Then annotate them in PDF and DT creates a new folder called Annotations which, if you have added the links that DT lets you create, will take you straight to the spot in the PDF that is referenced in the annotation.

…but I can give it a try.

Pick your reference manager, Bookends or Zotero. I use Zotero. Add your references to the ref manager with the PDFs attached:

Now, in DEVONthink, add the folder where your reference manager stores PDFs (~/Zotero/storage) as an indexed folder:

Now, annotate the PDF using the application of your choice (I use either Preview or DT–and sometimes I open them from DT and sometimes from Zotero–it doesn’t matter) and DEVONthink will display those annotations and allow you to jump right to that annotation:

There may be other steps that others use, but hopefully that helps a little.

EDIT: spelling errors


Continuing the discussion from DEVONthink with Zotero Workflow:

Thanks so much - brilliant. Now I just need to work through all the orphaned pdfs and refs that have arisen since I wrote my diss…
Again, thanks so much. Ngā mihi, Lindsey

Bookends is wonderful in many ways. Sadly legal citations isn’t one of them (eg. US ‘Bluebooking’). For the non-tech-minded user, Zotero is far easier in this respect.

Welcome @Legalista

Have you made a feature request to the Bookends people about the potential for improvement in this area?

@BLUEFROG Yes, thanks for the suggestion. I did this and I received a very nice reply. Sadly it said: “Unfortunately we have no Bluebook formats. … they are complex and arbitrary, and there are some things that Bookends simply can’t do…”

I first bought Bookends years ago and bought updated versions several times as liked it very much. Reluctantly, I swapped to Zotero because it does support the legal citation formats I need. Bluebook is the citation standard for most US law journals, and it was one of several legal citation standards I asked about.

I have a large library of highlighted PDFs in Zotero, and would love to be able to have it mirrored in Devonthink so that I could then link through to Tinderbox and Scrivener. I’m happy to keep using Zotero as the base for storing and highlighting the articles, but would like to be able to link them to related notes and other sources I store in Devonthink.

I have read all the forums for the various apps, and haven’t found a way to do this. It might be partly a reflection of my having no programming or technical knowledge, so I don’t understand some of the technical language used in some of the forum discussions and need a simple off-the-shelf solution.

If anyone could possibly point me in the right direction, my research and I would be exceptionally grateful :pray:

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Have you tried this:

Have you ever considered Paperpile? I use it integrated with DT3. Very easy to use. It seems it has what you need: Paperpile Adds Support for Legal Reference Types - Paperpile

@rkaplan Hi, and many thanks for the link. This was actually one of the suggestions I had spent a while looking at in the past, but it required more technical know-how than I possess.

I had been excited and full of hope when I saw it, but unfortunately the instructions were too complicated. Sadly I have no computing background and the instructions were like trying to read another language. I had no idea how to even start to try to follow them. I tried doing Google searches to find out what terms meant, but without success. I therefore gave up on this approach as it was beyond my limited abilities to implement. :cry:

@Silva Hi! I hadn’t come across Paperpile, so I’ll definitely look into it (while I’d prefer to stay with Zotero, which otherwise works well, I would dearly love to be able to sync my PDFs in Devonthink). Thanks so much for the suggestion😀

Hi, I hope it’s ok to reboot this thread for a quick question.

I am a clinical researcher in medicine and my workflow for some years has been to use Paperpile as my citation manager, allow it to store the PDFs in Google Drive, sync the Google Drive folder to my Mac, then index that folder so that the PDFs are in DT3. My entire academic life lives within DT3, so this is where I read, annotate, mark-up and cross-link academic papers. Of course, the reliance on Google Drive within this set-up has always been the weak point and in recent times Google Drive has changed its folder structure on more than one occasion, which means that all my carefully curated links within DT3 keep breaking. The other downside to Paperpile is that it continues to require a Chrome-based browser, which means that I am forced to use Chrome (which I’d rather not) or Brave (which I’ve been using recently but is a nuisance for some purposes); frankly I’d rather use Safari.

My main need for a citation manager is to harvest references while I’m using PubMed (or Google Scholar etc), find the relevant metadata (nb I’m not a huge metadata geek but it’s nice to at least get the reference right), access and download the PDF via my academic institution and put it in a place where it can be automatically indexed (or otherwise imported) to DT3, and then work as a citation manager when I write papers. I generally write papers in Google Docs (for ease of collaboration) but almost always have to revert to Word for the sake of some co-authors. Everything else takes place in DEVONthink.

Paperpile has done most of this well but the pace of development seems to have slowed. And the constant breaking of my DT3 links thanks to the Google Drive issue is hurting me. So I’d like to switch. I have used Zotero in the past (and, incidentally, wasted a very large portion of my time trying to hack solutions for marking up PDFs on iPad, but this was many years ago) and still have an account. I’ve never tried Bookends.

Is Zotero still my best bet to switch away from Paperpile and otherwise maintain (approximately) my current workflow. Or are there specific advantages to Bookends that I haven’t appreciated in reading this and other fora? Or is there an even better solution?


If you use Zotero, install zotfile for putting the PDFs in other folders, which should be indexed by DT. That way, you can annotate with your iPad in DTTG. Otherwise, the PDFs are scattered in cryptic folders in the main Zotero folder.


I prefer Zotero’s PDF annotation toolkit over DEVONthink. FYI there’s an iOS/iPadOS app for Zotero and an Android app is in development, which will be great for android-based e-paper readers.

DT adheres to the recommended spec for PDF annotations, but this was causing problems with corrupting the text layer of PDF docs, especially on mobile or when using an unstable web connection (ie. when I’m reading/annotating on the subway). Zotero uses a non-standard format for PDF annotations, storing them in a sidecar file rather than embedding them in the PDF doc itself. This has the benefit of being quicker to upload to the cloud, especially when working with large files, because it never makes changes to the PDF itself. So far Zotero has never corrupted my PDF files, while DT was a common culprit. I still index my Zotero data file within DT and I sometimes prefer DT over Zotero when running advanced searches on my database of research articles, but I do all my annotations/markup in Zotero.

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Thanks for this very helpful advice. I’m still vacillating.
Zotero is much harder to get to work with my university’s OpenAthens access to full-text academic PDFs (it’s seamless inside Paperpile) but I’m also attracted to Zotero’s integration with Research Rabbit.
Looks like there is still some productive procrastination ahead.

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I don’t like the performance of Zotero’s PDF Toolkit. Scrolling is not smooth, and pinch to zoom and scrolling does have a lag.
Having non-standard PDF does have its problem. But yes, it is also an option.