I’m an academic who’s a longtime user of DT on Mac, but only recently started using DTTG on iPad. I’d love to hear from other academics about what your workflow is for annotating PDFs from DT on your iPad.
Currently, my workflow for reading PDFs in DTTG is as follows:
Color-coded highlights: yellow for general stuff, light blue for definitions, light green for important stuff I want to come back to later, and light red for places where the author is objecting to another person’s view.
Add color-coded notes.
Use summarize annotations in DT4 to create a markdown file with my highlights and notes, where I then take a second pass to add any new thoughts, etc.
The major pain point for me is 2: adding a note in DTTG and then typing it on iPad is much more laborious than simply handwriting a note in the margin, which is what I would normally do if I were reading a book or article in print. A more minor note is that switching and customizing highlights colors is not very fluid in DTTG, but from what I’ve read here those features are made by a third-party developer and are somewhat limited by Apple too.
I’ve been thinking about getting an Apple pencil so I can use Apple’s “Scribble” feature to handwrite notes in DTTG, so I’d especially love to hear if people find the Apple Pencil useful. I’ve also been considering using GoodNotes or PDF Expert or another app that will allow me to handwrite notes in the margins (though as I understand it, “Summarize annotations” in DT4 will not capture these), but since my files are indexed rather than imported, I’m a bit hesitant to do anything that would clog my DT database with multiple versions of the same article/book.
I’m curious to hear what other academics use for their PDF reading workflow so that I can learn what works well for others
1–3 is pretty much exactly what I do, except that I also use underlining a lot; Summarize Annotations helpfully distinguishes them, so you’re not limited to highlight colours. iPads are brilliant for touch annotation, but less good for any kind of written notes, so I tend to use the iPad when I’m reading something through the first time and just want a distraction-free, uninterrupted experience where I’m just doing finger markup as I go. If I want to take notes, though, I’ll use DT desktop.
Not an academic example, but today was the day the London Film Festival programme dropped, so I went straight into my annual workflow for this:
Go through the PDF version on iPad, highlighting titles I’m interested in, and underlining the showtimes and venues for each.
Sync to desktop and Summarize Annotations to Markdown (sometimes Sheet is best, but I’m enjoying the new Markdown editor).
It’s then a fairly simple series of text munges to turn the Markdown file into a Hyper Plan calendar view and see which screenings clash so I can embark on the annual Sudoku of figuring out which to book. (And yes, the Borges doc really is five and a half hours long…)
I’ve updated the Hyper Plan link above to the SummerFest discount, which dropped yesterday somewhat later in the season than usual. (No, DT isn’t in it this year, but other favourites like Hookmark, Scrivener, and Mellel are, as well as Hyper Plan developer Andy Brice’s flagship app Easy Data Transform.)
I don’t have anything as organised a system as you do in terms of disciplined coloured highlights, though I have aspired to it.
I read everything with Apple Pencil in hand. Though I really balked at the cost, it’s been rock solid and I couldn’t do without it now. My daughter has a knock-off pencil, and frankly it is quite good. You could try one for 15 dollars/pounds/euros or so, and see how you go before you shell out for the AP. Apple’s Scribble feature has never been reliable enough for me. I do, incidentally, take all my meeting notes on the iPad as well using Nebo Myscript. This has very good handwriting recognition, even of my ever-deteriorating hand (it is much better than Apple Scribble), and so I can save the handwritten notes to PDF with a decent enough text layer for searching. These are also stored in DT. I loathe pasting sticky notes onto the PDF. I have used Goodnotes and Notability in the past, but DT2G has a VERY GOOD mark up engine, and I don’t need anything else. I haven’t even upgraded yet to DT2G 4 (don’t tell the fine folks at DEVONtechnologies …).
Much of my reading tends to involve highlighting, and annotation. I most do these things:
demarcate the structure of an argument (using hand drawn brackets) – just the way that my brain works
highlight material that will allow me a to quickly take in why the materials was important for me at a certain time, when I asked particular research questions.
scribble in the margins: zoom and a finer nib allows for a remarkable amount of space even in smaller margins.
I do not extract annotations, but instead have a note-taking system in Obsidian running alongside the reading in DT2G. I find that the time between 1) reading the PDF annotating liberally, and 2) extracting what I need in a short RN gives exactly the right amount of friction to decide what really matters. In Obsidian I keep RNs (reading notes, 1 per source, where I honour the thrust of an argument), and CNs (concept notes, where I break down critical ideas and might link to a whole host of different sources). Importantly for me, I preface all my RNs with a link back to the PDF in DT, and I love how these links work across Mac and iPad.
I import everything and sync through Bonjour (after years of relying on a Dropbox sync, I don’t know why I bothered, since my phone, iPad, and Mac are always in the same room with me).
Thank you for sharing! If I’m following, it sounds like you read in DTTG, and when you want to add a note to the PDF you’re reading, you zoom in on the margins and handwrite the note there with your Apple Pencil (instead of adding a “note” in DTTG).
I’ve been thinking about getting an AP and trying a similar workflow. What’s holding me back is that I personally really like the “summarize annotations” feature—though I realize you said you don’t use it—and I wish that it would capture handwritten notes that are written directly in the margins (i.e., written without using the sticky note feature).
That’s exactly right! I did want handwriting capture for a while too, but realised that my notes don’t really need to be searchable in that way, and certainly are rarely profound enough. Annotating and highlighting is often for thinking and processing in the moment. If there is anything worth writing out for posterity, it goes into Obsidian’s system.
Reading this made me reconsider what my process really needs. While I still think handwriting capture would be a nice-to-have, I’m coming around to the idea that I don’t need it.
Given the updates that have recently been made to markdown files in DT4, I’m thinking I might use your idea of reading notes and concept notes but keep them in DT rather than using Obsidian. I used to use Obsidian, but I stopped because I noticed I was putting pressure on myself to add atomic notes and links, until it felt like I was just taking notes for the sake of taking and connecting notes. (This is not to cast any shade on your own process ofc—each person should do what works for them!)
Hope it goes well! On the ‘pressure’, don’t let just my comment be another spur to change your system in the everlasting quest for the perfect system. The whole note-taking, PKMing, Zettelkasting, YouTubing influencer crowd has a lot to answer for in terms of generating anxiety for a whole new generation of budding writers, thinkers, note-takers, and knowledge workers! I don’t do half as much connected and atomic note-taking as I might, but neither do I care (anymore).
For what it’s worth, I too could probably have all my md files in DT, especially with the nice new improvements to markdown rendering and themes. Some people prefer to have their notes right next to their source files in DT and there is a lot to be said for that, and of course, for keeping it all entirely in one system. I still prefer Obsidian for a few things DT doesn’t do easily (and shouldn’t do!), but I don’t think it would make the blindest bit of difference to the quality of my scholarship.
Then I am quite the dinosaur anyway given the direction of travel on the app, and on this forum: I have yet to hook up an LLM to my database, I have yet to query my databases via a finely crafted prompt, and I have yet to master an Apple Script, etc etc. DT is just a really great organisational tool for me.
My system is fairly solid for me now after a couple of years of tinkering (which I suspect ultimately brought me back to where I’d started ). It’s very similar to yours, though not quite the same:
Highlight key sentences in the PDF (I do not do any colour-coding).
Annotate with thoughts as I go, using Apple Pencil and occasionally typing, depending on my mood.
Use the summarise function on DT to turn my highlights into markdown notes. Tidy up and add commentary where necessary (at desk on DT).
It’s basically just a more digital version of how I read a book. I do nearly all my PDF reading on iPad, I’m not really a fan of reading papers on my monitor (never have been). I’d love to be a super-organised person who has colour-coded highlights, but I’m not. Everything gets highlighted the same colour and I read with pen in hand. As with books, most my marginalia are just thoughts as I go. They’re not really intended to become ‘permanent notes’, they’re just me thinking about things as I read.
The ‘bulk’ of the work happens when I convert the highlights to markdown (honestly it’s such a little tool in the DT box but it’s what made DT a game-changer for research, for me). At this point I set about arranging the highlights how I want them (sometimes they stay in the order they appear in the text, sometimes I restructure them under different headings). I work through the markdown slowly, adding comments if I want to, and cross-referencing with the original PDF to re-read my marginalia and add what I want in the final note. Usually I just have one markdown file per paper, but sometimes a paper is complex or interesting enough to warrant me breaking out the ideas into several separate notes. This is rare but happens occasionally.
While I will often go back to the original paper if I need to, these ‘study note’ markdown notes are usually my main reference source when I’m looking for info. I trust my past self to have done the work to turn the paper into something relevant for me.
(This is actually just a more sophisticated way of how I did my dissertation and thesis back in the day, with pen and paper, hence my comment that after much tinkering I’ve ended up back where I started!)
I have the free version of PDF Expert. Its main use (which DTTG could think about offering!) is to add a margin to papers that are ungenerous with their whitespace. If I think I’m going to be annotating heavily, I will add a margin to the PDF at the beginning and save myself a headache later on. Publishers who use tiny margins on papers (and books) should be banished to a library with no filing system, cursed to wander forever.
I don’t really use PDF Expert for reading. DTTG does everything I need and I would just the doing the same things in another app. When I do venture into it for reading, it’s usually just because it’s a huge PDF and it felt easier to have it standing alone in a separate app to DTTG (where I might be interacting with other files in the meantime) or because I was feeling whimsical.
I know, thanks! I tend to be a late adopter, never quite finding time to make the jump, worrying about breaking a system that works just fine under the work pressures that seem never to ease off. I just updated to iOS 27 and iPad OS 27 perhaps four weeks ago, and am still rocking Sequoia.
My Pro license also just lapsed but I will renew this weekend (honest…). I could have done all of this AND got DT2G up in running in the time I took responding to these posts
This is a typically generous example of your workflow @MsLogica, thank you. Maybe I am the one who should be looking into exporting my PDF highlights to md notes via DT as you describe here! It does sound simple and compelling.
So I finally shelled out for a (used) Apple Pencil and have been experimenting with it. I really like it for highlighting, and it’s also nice for writing in the margins. (h/t to @SebMacV for suggesting zooming into the margin and using a fine nib!)
That said, I still run into a major pain point. It’s really nice to have my notes captured by “Summarize Annotations”—the resulting markdown file is invaluable as a reference document. But to get a note captured, I have to use “Add Note” (as mentioned by @DTLow ), which means either typing (agonizing on iPad) or using Scribble in the tiny text entry field (impossible). Here’s how much room that field gives you:
So in practice, handwriting notes isn’t viable there, and I’m back to typing.
What would make an enormous difference for my workflow is simply a larger writing area for “Add Note”—perhaps via a toggle in settings, or something that auto-enables when a stylus is connected. Right now, as far as I can tell, there’s no realistic way to handwrite into that space. (Please let me know if this is already possible—I’ve been looking across the documentation and fiddling with stuff like switching to landscape, but I haven’t found a solution.)
A more minor point, which I realize may well be out of the developers’ hands: Apple’s Scribble recognition is noticeably weaker than what GoodNotes or Nebo manage, and at this tiny field size the two problems compound. If there’s any room to improve handwriting recognition there I’d welcome it, but I’d be happy with just the extra space.
To be clear, I’m not asking for freehand marginal annotations to be OCR’d—I understand those aren’t real annotation objects. I just want the existing “Add Note” feature to be usable with a stylus, so that I can marry the fluidity of writing by hand with the extreme power of “Summarize Annotations.”
This doesn’t solve your problem (sorry!) but just for clarity: using the “Add note” function isn’t the only way to add a typed note to a PDF. You can also just add a text box to the document and type in it. Like text boxes in other apps, you can resize and play with font, colour and size if you so desire. You can also set a background colour for the box and a border, if you want your typed comments to stand out. When I type annotations I actually do this (I don’t like the “add note” function in PDFs generally). DT and DTTG will remember your default text box settings, if you’re a person who likes consistency across your files.
When it comes to summarising annotations, DT will pick up any text boxes you’ve added. However be aware that it compiles the annotations sequentially, so if you want your annotation to appear below your highlight you need to position the text box slightly below the highlight it refers to, otherwise the comment might end up above the highlight in your annotation file.
). It’s very similar to yours, though not quite the same:
