DEVONthink with Zotero Workflow

I also use both Devonthink and Zotero. I use zotero to hold my pdf files and to categorize my sources in a single source folder without worrying about structure, which I can move around within zotero. I use Devonthink as my notes repository. I actually don’t index my pdfs in DTP3 because they are a bit too large and are held in an iCloud folder to save space on my mac. (Although I imagine indexing my pdf files in Devonthink would improve their usefulness!)

I’ve found Kourosh Dini’s taking smart notes with Devonthink to be helpful! It is definitely worth a read. It walks you through the steps of creating a note, creating a link to zotero, and linking notes.

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Thanks: I don’t think I’ve looked carefully at that pull-down menu for several updates.

That said, I’m not really sure about the utility of importing Bookends metadata. Would rather be able to export my DT metadata into a cite-able format.

Thanks: I’ll try to find time to have a look at Kourosh Dini.

I have a similar set-up, using Zotero to store journal articles, ebook .pdfs and other items where metadata can be downloaded directly into the app. Most of my note taking in DT3 includes internal links to items stored (or indexed) in DT3. It can, however, get very fiddly and time-consuming.

I use Zotero with DT. This is because I need to work across platforms with people who may or may not invest in software. I can fund the cloud space and work with groups. Zotero provides an easy way to share core resources with co-authors, and pull a formatted reference. However, a reference is a likely to be in Scrivener if I’m note taking on something specific I’m writing. DT is my go-to for storage and retrieval over time. I’ve always wished DT would save me a ton of effort by simply adding the reference management functionality. I almost never do an end of project substitution of references for tags. Much easier to use the A-D formats and just do them as I’m writing. Zotero just gives me an easy way to do the first-time citation and build a project bibliography. IMO the days of “ob cit” are over. In fact, often the URL is often important for the convenience of readers, also for in-text citation. But I mostly do consulting writing and my readers want convenience rather than citation elegance. I would say that in some cases with document acquisition it makes sense to collect documents into Zotero first from those sources that will support the transfer of citation meta data automatically. However, so much of what I work with comes from sources that do not facilitate this, I often end up making a manual entry anyway. It’s amazing how many document creators don’t include clean document info, even, for a PDF.

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This is sadly true, even for so-called professionals.

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I tried Zotero and there was much I liked about it, but, ultimately, the non-native UI was just too much friction. (The same holds true for Obsidian.) I use Bookends to organize my PDFs of articles and books, and to generate bibliographies for work I do in Scrivener. I take notes on those PDFs in DevonThinks because it is, to be honest, 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.

This is as close as it gets to blissing out while taking notes.

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I am familiar with Zotero but have been using ReadCube Papers (still in Beta), which is destined to be the very best reference manager going around. And I’ve used them all. I would love it if Devonthink was able to create .ris for media articles and so on (for which I’ve curated pdfs) and export that information to ReadCube Papers. I have tried to do this with Bookends and then on forward to Papers, but it is a lengthy and convoluted process. If Devonthink had the capacity to create .ris (or similar) outputs for all file types (obviously with some manual adjustments as needed) it would be hands down the software of choice for (Mac user) academics globally. Because that would allow greater versatility between curation of content outside a reference manager (i.e. web pages, tweets, media articles, and so on), followed by the export of citation details to that reference manager in order to cite the materials in manuscripts written by academics. Reference managers do a good job of downloading academic papers with DOI numbers, but they’re very poor in terms of curating anything else. That’s where Devonthink is so brilliant at capturing. If DT could convey to my reference manager what the citation details are (using .ris or similar) it would be a workflow dream.

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@DarylAdair
Interesting - what features are upcoming from the beta version which have you so enthusiastic?

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!

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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.)

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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.

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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

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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: