Use of DT for Research and Note Linking - What works for you?

I am using the launch of DT3Beta as motivation to try and use DT again as my main location for PDFs associated with my research, as well as notes on them and other ideas. My current workflow is gathering information from PDF articles that are relevant to the manuscript we are writing, taking notes separate from the PDF, and trying to stitch it all back together in the end using references in Endnote or some other horrible bibliographic software.

This is a standard academic workflow, made more complex if larger documents (review papers, books, etc.) and references of course are utilized for more than one manuscript.

My question is how to do this better using DT3. Is there a good way to link notes back to a PDF that I am missing? Is it visual in some fashion (i.e. can I see all the notes that I linked to that PDF somehow.) I know this application can be used in a better way than I have been, but am looking for guidance how. I tried to do this in Tinderbox for a while, but it frankly took too much energy to maintain, and couldn’t export things in a usable fashion in the end.

Would love thoughts from folks who are commenting to themselves on other PDFs and using that information to generate future manuscripts, etc. and how they have used DT3 and maybe some of its new features to accomplish this simple task. Thanks!

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I don’t do the kind of thing you are discussing, but I’d suggest you start with Tools > Inspectors > Annotations & Reminders. :slight_smile:

This looks like an interesting solution - can anyone comment on how they use this in a research work flow?

I would like notes that can be linked to multiple PDFs, but I am not finding an intuitive way to do this. Perhaps this is not DT’s forte, but if not would love suggestions from others on where to turn. Somewhat surprised this isn’t a common ask.

Somewhat surprised this isn’t a common ask.


These forums are full of such discussions - and many other interesting things.

I use DT as a complement to my law library (which is otherwise in Scrivener and Finder folders containing thousands of pdfs.)
I’m not into annotation, but I am into smart groups and tags.
Gathering info from a pdf is simply (ha!) a matter of either copy/paste into a RTF note (plain text if you prefer), rename the note the same as the pdf for sorting with appropriate tags, and/or tagging the note and pdf. Smart groups I use either to gather tags or phrases.

For example, I’d use the phrase “presumption in favour of reality” as the name of a smart group, enter that phrase into ALL Matches, for a search on all pdfs and notes. After performing the search, ie creating the smart group, I could then view each pdf and add appropriate tags for any other key information or not.

As for notes, tags don’t have to be words. If for example you tag a pdf 0001 and tag a note 0001 a smart group to search for tag 0001 would contain all pdfs and notes with that tag.

For caselaw, I also use smart groups, naming the group, for example: 4-6 Trinity Church Square Freehold Ltd v The Corporation of the Trinity House of Deptford Strong [2016]. With smart group search Match ALL I enter Trinity AND Deptford. Any pdfs or notes containing those words but nothing to do with the case I would then edit the smart group to exclude a word or two that would exclude the unwanted result.

As for generating future manuscripts, etc, DT can be used for writing from scratch. Use of tags and smart groups can keep all the info together.

Not only the forum, but the world is full of interesting bloggers and discussions of using DEVONthink in an academic / research / legal context. Google is your friend.

Look in the forum and branch out here…

DEVONthink and academic workflows …

Read the DEVONtechnologies blog for lots of other links to researcher and writer commentary.

Doing research with DEVONthink’s help is, IMO, one of the highest and best uses of the product.


I also use a a loose assortment of tags and smart rules in DT to cluster my notes on a single text. PDFs are all in Finder, indexed by DT (and synced across machines by Box). Setting out even one or two project-specific tags fairly early in the process usually helps.

When I’m writing, I use Scrivener as an intermediate stage, in which I actively gather DT notes (via copy item link), links to indexed PDFs in DT, and links to online primary materials in individual Scrivener notes. I can then work from those aggregate notes.

DT3 is proving particularly useful with its smart rules/groups at organizing stuff I’ve assembled for years before I started using DT.

What I was saying was that I was surprised that there weren’t already features in DT3 that allowed you to link multiple notes back to a specific PDF visually or in groups, and that I was also surprised that this isn’t a common request, as annotating PDFs is a common workflow issue.

Following some of the helpful links below, I found much the same result as 5 years ago when I checked into this, as did many others - and found my own post from then!

So basically what I was asking is have any of these features been implemented. It sounds like most people are using a mix of tags/links to do this on their own, without the app supporting a visual linked view for this. May be beyond the scope of the app, but still what I wish for when I am using it.

Please let me know other solutions as well, will try to implement the manual version in the meantime.


Jul '14

Thanks so much for this. Yeah, I’m actually looking for some kind of built-in feature in DEVONthink to do this because…it would enable me to look an an annotated PDF document so that I could reference the comments and mark ups in its corresponding Annotated File (in DTP). Make sense? It seems like a relatively simple feature to create (since other apps have them), and it would sure make it much, much easier to work within DTP to accomplish annotation tasks.

Anyway…I’d welcome any other suggestions. And I hope DTP developers note this suggestion! Thanks.




Aug '14

I understand that one needs to use Skim to view highlights and comments in PDF documents (though I hope DTP develops built-in features that enable us to do this). But is there any way to more easily select and copy the comments that are embedded in PDF documents? Thanks!



Aug '14

Not yet possible but planned for upcoming releases.

You can see and edit a connected Annotation file in Tools > Inspectors > Annotations & Reminders.
You can see the annotations in a PDF in Tools > Inspectors > Document > Annotations.

These are both covered in the Help > Documentation > Inspectors.

Does that help?

Yes - this is great! So glad that this has been included in the new version, will start playing with it.

If anyone has worked out a good system of linking annotations together but with connections to the original PDFs intact, I would be interested to hear how people have been using this new tool.
Was hoping there was a way to link notes/annotations visually somehow, but will play with the new feature first and see if that works.

Any further documentation/discussion threads of people who have been using these features for a bit and have a workflow would be great! If anyone has a workflow with MarginNote or something like it that works with the new annotate inspectors would be interested.

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The research I do doesn’t come from PDFs, but from RSS feeds. So my method is a little different. It’s a little complicated right now, but it’s working for me now.

(1) I use Feedly to manage my RSS subscriptions and do my main research. Their Pro version offers the ability to add highlights and notes to the articles you save, which is quite handy.

(2) But I need to get those notes/highlights out of Feedly, so I use the web tool IFTTT (If This Then That). I create a trigger in IFTTT whenever I add a highlight or note to an article in Feedly. IFTTT will record that information in a new text file on Dropbox. Each article gets its own file, which includes the title, URL, and the information I highlighted or noted. (I also have IFTTT add this information to a Google Sheet for easy review and sorting.)

(3) I then index that folder in DevonThink, and add document links from those files to any writing I am doing on that subject.

I’d prefer to not rely on so many different apps/services, so if anyone has suggestions for streamlining this process, let me know!

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I don’t use Feedly, but what benefit does it have over using feeds in DEVONthink?

I started with Feedly back when Google Reader was shut down. I love that it has a very reader-focused interface: reading articles is very comfortable (even on a phone), and they have layouts that make it very easy to quickly review a tons of feeds. I also appreciate it being web-based, so I can access feeds (along with all my saved articles, notes, and highlights) from any computer or my iPhone.

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Interesting! Thanks for the opinion on it.

Hi Bluefrog

Am I right that although you can view these annotations (eg highlighted passages) in DEVONthink 3, they’re not addressable by Applescript? I used Script Debugger to look at a PDF selected in DEVONthink (3b3) but I don’t see anything there.


That is correct. In-document annotations are not accessible in AppleScript.
Development would have to weigh in on the feasibility of adding this function.

That’s what I thought. Thanks.

For context, I currently annotate / highlight in Bookends or Highlights then use Highlights’ export to DEVONthink feature to create a set of notes, one per highlight. I then have a script to tidy them into a particular format, add metadata etc.

If DEVONthink exposed the highlights (including highlight colour) and annotations to Applescript that would streamline the process.

That said, my current setup - still a work in progress - works, so I’d understand if this wasn’t prioritised.

Thanks again.

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No problem. :slight_smile:

If you’re looking for more visual connections , you might try mindmapping apps. Obviously, this would exist outside of your DT database – but could be another conceptual layer of notes about various sources. The good apps let you even import attachments to nodes so you can have those PDFs right there as well.

So basically the system would look like:
-DT for a well-organized, tagged, grouped, list of PDFs and annotation notes (with each PDF linked to annoation file through the inspector )
-mindmap for connecting multiple sources together and organizing the source library as a whole.

I recommend MindNode for this. This is a system I am currently exploring

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Welcome @Clayman98

Thanks for the input on this. :slight_smile: