iPad PDF annotation app with markdown export

I am on a search for the next best PDF annotation app for my needs. I’m posting an opening for others I know on this forum who have comparable interests.

  • It must work on the iPadOS platform. I find this platform to be far more efficient for annotation and markup than working on macOS.

  • It must allow highlighting and image-selection/capture as a minimum.

  • It must allow the user to add notes to the annotations.

  • It absolutely must allow the user to export the annotations as a markdown file, including images. This is my make-or-break criterion (I am heading toward using Obsidian for the review process).

  • It should allow the user to add tags to the annotations.

  • It should work dynamically to share with other i(Pad)OS and macOS apps such as Devonthink or Bookends.

  • It should be “light-weight” (meaning that it should just do annotating well and export its results, not also contain the mapping/studying features as in LiquidText or MarginNote).

I have two current contenders, Highlights and Zenreader.

→ Zenreader, the new kid on the block, meets my absolute requirement but does not currently have an iPad app. As a new kid, it is also rather clunky in its implementation. It appears to be an electron app (which does not bother me).
→ Highlights has an iPadOS app but does not meet the absolute requirement directly. A round-about way to meet the absolute requirement is to export the markdown to Devonthink and then export/link that content to Obsidian. Highlights has its own annoyances, but I can overlook them if it only exported the annotation set directly to markdown.

As an aside, I will test MarginNote (since I have it) if only to discover whether annotations can be exported as markdown. In my initial tests over a year ago, I found the annotation features in MarginNote to be exactly what I’ve wanted. I have however been seriously put off by being locked in to its storage format. I see in the meantime that a plug-in exists to support markdown export. Let’s see where this goes.


JJW

Doesn’t Highlights export directly to n markdown files? It used to.

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PDF Expert exports into MD… not sure about images, as never had the need to check

I couldn’t find where PDF Expert will export to markdown on the iPad. It can export text in the MacOS app. In the iPad app, I have to export to an .html file, open that, select all, then move it into Drafts. It’s a few steps, but it ultimately gets the job done. Unless it does export to markdown and I missed it… then I’d be very happy.

The direct markdown export form Highlights does not include images. The markdown export to Devonthink does include the images.


JJW

I was frustrated by this too and submitted feedback to Highlights’s developer, but I have yet to see them act on any feedback (from me at least)… :upside_down_face:

Nonetheless this workflow is, far as I know, the best current iPad-based option.

Liquid Text meets most of this - but doesn’t meet Markdown export. :frowning: (I wanted this also.)

Thinking slightly laterally, I wonder if any of these export in a format that could be converted to Markdown. I shudder a little when I say this but that might be RTF.

There is a post of @drdrang at his blog in which he copies his LiquidText notes to Drafts, and applies a JavaScript cleanup script. Then the notes are at least in regular txt format (so moving to (maybe very basic) markdown version would not be too far off).

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I use highlights and I do markdown export directly. To get it into Obsidian I just move the files into my inbox folder in my obsidian vault.

My workflow is

  1. do all my annotations (highlights and notes) on the iPad.
  2. use the share button at the top and send theplain text (markdown) annotations to my mac via AirDrop. They are put into my download folder on my machine. From there I can either drag them into the Obsidian vault into the folder I choose or use Hazel to move all things with a .md suffix to the vault inbox. I’ve tried both and I use a manual approach right now because I am doing a lot of testing of markdown files that I do not want to move.

I can see and link them in Obsidian or add more notes.

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This works for everything except images.

I need images too.

Digging a bit deeper, one can discover an interesting inconsistency. The images exported to Devonthink markdown (which works) are in an assets folder as JPG. The images referenced in the direct markdown export (which does not work) are to be in the same assets folder but are referenced as PNG. So …

Yes, even MarginNote has a lateral method through docx → cut+paste (see the MarginNote forum where I posted a request also for markdown export). Their approach leaves the figures referenced to the user library container folder that MarginNote uses to store its internal assets. Ugh!

The cleanest approach appears to be Highlights → Devonthink → (find the asset folder, copy it to Obsidian, change the PNG to JPG) → Obsidian.

I might also hope that, through this thread, more folks who are interested in this workflow would also ping the developer. As I noted in my email to him, given that it works with Devonthink, he has the code base developed, he just needs to (figuratively speaking) throw the right switch condition.


JJW

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I see, I hadn’t had a need to save the images in Obsidian. I’ve only had notes attached to images so I had never tried to pull the actual images into my Obsidian folder.

I’ve just sent a request to the developer too. I can see how it might become useful in the future. Most of the PDFs I annotate don’t have lots of images.

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@oldblueday you are correct, and my apologies… the Mac version exports to MD, but not the iOS

FWIW… I just received an email from the folks at Liquid Text, getting thoughts on a subscription based model for sync and support… I’m kinda meh on yet another subscription it this point…

Totally sympathize, as I’ve been seeking out a better option. I followed up on your zen recommendation on another post, and have been a bit lukewarm on it. Can I ask, why don’t you simply run an ios shortcut to send all relevant images to an obsidian folder? (And on IOS, you could simply copy and paste, or run a KM macro). If everything hangs up on that, this would be an easy fix, and you could essentially use the free version of many of your other PDF programs that offer markdown. Or is that you want a fully integrated approach?

If I was solely macOS, I would likely do Zenreader over Highlights because Zenreader has the Outline option. It is nice to do some pre-layout of the annotations directly while reading the PDF itself.

Yes. I can program shortcuts or Applescripts or something. And I likely will soon enough from Highlights through Devonthink to Obsidian. But this should not have to be so hard that even an unexperienced user could not just direclty dump out a markdown file and move into a different app.


JJW

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Updates

  • Zenreader flattens annotations from other apps when it imports PDFs. I experienced this failure some time ago with LiquidText, and it is a show stopper for me.

  • Highlights iPadOS allows you to delete PDFs that belong to other apps. Simply go to the Recents list, select a PDF, and delete it. Not irreversible → go to the Recently Deleted to Recover.

  • Highlights iPadOS is only modestly better than Bookends for annotating.

  • Highlights iPadOS exports/shares to Devonthink iPadOS using HTML with no option to change this to markdown.

  • Highlights macOS exports markdown annotations into Devonthink but names the main file with an extension .markdown (rather than .md).


JJW

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Just to add to your data: PDF Viewer is another contender. It can take image annotations. It can export markdown notes on iPadOS and iOS. However, the export doesn’t include images.

Have you seen this?

Further Updates

Continuing my explorations, I’ve learned that …

  • Highlights macOS will export annotations as TextBundle to include all assets. This is a FOLDER.
  • Highlights iPadOS will export annotations as a TextBundle to include all assets. This is a PACKAGE.

This essentially means that I could bypass Devonthink as an intermediate translation step (but I will instead explore indexing the respective Obsidian folder in Devonthink). What remains to get the annotations properly into Obsidian (and Devonthink) is …

  • Assure that the TextBundle is a folder not a package (through a shell setfile command)
  • Assure that the internal file in the textbundle folder has an extension .md rather than .markdown (Obsidian does not recognize .markdown files)
  • ? Remove the .textbundle extension on the folder (just to make the folder title cleaner in Obsidian)

I have a script in the Devonthink forums to handle the second two steps (in case anyone has textbundles in DT).

Finally, Bookends and Highlights do not formally support tags on annotations (ZenReader does, as do MarginNote and LiquidText). I’m using #hashtag notations directly in the note field for the annotations themselves (#why, #how, #result, #equation, #insight, #idea). The markdown export process hides the #hashtag in the annotation URL as ![#hashtag some text]( … link reference …). I’m working on a process (through BBEdit with REGEX) to massage the “hidden” tags back out of the annotation envelope (converting ![#hashtag some text] to #hashtag some text ![some text]).

AppleScript is your friend in handling all of this.


JJW