Annotation → Markdown Workflow Help?

I am hoping to find a workflow to support academic research and note-taking.

  • sync a PDF between my MacBook Pro and my iPad Pro
  • read, highlight, and annotate the PDF on my iPad or my MacBook Pro
  • export the highlights and notes to markdown
  • access markdown in Obsidian

Tools I’m already using

  • I like to look for academic articles using Research Rabbit.
  • I add PDFs I am interested into Zotero
  • I would like to read the PDFs either on my MacBook Pro or my iPad pro, adding highlights and taking notes.
  • Zotero already allows me to extract my notes and highlights into a markdown file, when working on the laptop, but if I need to use another application to do this on the iPad, that’s ok.

I tried adding PDFs to my Kindle app on the Mac, but those don’t sync to the iPad, as far as I can tell. If they did, I thought I could use Readwise.

I’d also like to do the same for blog posts, online articles etc. (highlight, annotate, export to markdown). And in my dream world, take notes with timestamps on YouTube videos that I can export to markdown.

Zotfile has some functionality for round-tripping PDFs built in.

There’s also Papership, which seems to be languishing. (Last update 2yrs ago.)

Finally, Zotero is working on an iOS app (currently maxed out on beta testers).

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There is a plugin called PDF Highlights that might do all you want within Obsidian. It is by someone called Alexis Rondeau. He explains it somewhat on his plugin page within Obsidian.

There is also a chrome/brace/edge extension called yinote that will allow you to take notes on timestamp videos on YouTube etc. There are a couple of others I have also used one called ReClipped. I have had varied success with this extensions

To download articles and websites look for an extension (chrome and paid for on safari) called Markdownload. It downloads text (including blog posts and articles) into mark down format.

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As @JohnAtl has already mentioned, Zotfile works nicely for me - I have it set to an iCloud folder and then access the files in PDF Expert.

On a side note, I sometimes use Skim for PDF note taking, as this appears to work on password protected PDF files as well. If only this worked on British Standards, which are now protected by DRM and will only open on the machine that you downloaded them on and in Adobe Acrobat… (as they use FileOpen DRM).

I’ve not tried it, but I believe LiquidText allows you to markup and make notes on web pages, and then export the notes. I tend to download any web pages now using SingleFile (extension for Firefox, Chrome, Edge) which downloads pages as single HTML file - far nicer than the Zotero download method.


I use bookends on my iPad and a shortcut to send all annotations to Obsidian. But this is super cool tool as a way to read and annotate within Obsidian in a driven way. Works on iOS too! GitHub - elias-sundqvist/obsidian-annotator: A plugin for reading and annotating PDFs and EPUBs in obsidian.
I think and either one of the free plugins or Readwise is the way to go for the other online content. (There is a student/educator discount for Readwise).

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I appreciate your suggestions, all! Off to experiment. :slight_smile:

You may find interest in these two apps.

Zenreader (macOS only)

Highlights (macOS and iOS)

The first one may feel more akin to what you hope to accomplish by using annotation tool plug-ins in Obsidian.



+1 for Highlights. It’s good for Markdown notes that live alongside your PDFs on Mac and iPad.

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+1 for Highlights – with reservations. Highlights is a subscription app, and is regulary updated on iOS and iPad, but the macOS version has not had an update for 9+ months, during which the other platforms received several changes.

OTOH, LiquidText published an update today – integration with Zotero. Haven’t tried this yet.

Subscription required ($95.99 USD/year)

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Zenreader looks interesting -thanks

I use Bookends to manage my references and it’s companion iOS app to read and annotate on my iPad Pro. I then use a custom AppleScript to distill my PDF annotations to a Markdown note, which also include the reference’s bibliographic data. My annotation notes are saved in DEVONthink 3.

This workflow is relatively new for me, but I’ve been pretty pleased with the results.

If anyone is interested in adopting a similar workflow, let me know and I’ll post my AppleScript (which is loosly based on this one by Ryan Murphy).


That is pretty much my exact workflow. Mine is still a WIP but here is what’s working so far.

Search for papers etc. via Academia, Research Rabbit and elsewhere.
Collect DOI links and add them to Zotero
For things I cannnot get easily via automatic DOI downoad, download the item in queston an manually add it to the Zotero reference
Use Zotfile and Zutilo to move the files to my iPad for reading and annotation using Highlights
Once back in Zotero export to Markdown into Obsidian
I maintain the un-annotated and fully annotated version in Zotero because I’m paranoid.

For kindle PDF annotations I export them via share menues but it’s painful and rarely works properly

I also do heaver use of GoodNotes on iPad then text recognize and then via a shortcut send automatically to Obsidian for clean-up and linking.

Thanks for sharing… which is the tool on the iPad you use for highlighting and sharing the PDFs that you have synced from Zotero?

Highlights on the iPad One ofhte few subscriptions i have and well worth it.

I have downloaded a Highlights trial on my iPad. In order to get the PDFs from Zotero, I had to setup a Hazel rule to copy the PDFs from the local Zotero folder to a folder in iCloud. Zotero freaked out when I tried to move the storage to an iCloud location. If there is a better/easier/cheaper way to do this… I’m all ears. Here’s where I’m at:

  1. Find article on my Mac using academic search engines
  2. Add PDF to Zotero
  3. Hazel copies PDF from Zotero storage location to folder in my Cloud drive
  4. After sync, open files in Hights

(haven’t tried this next part yet)…

  1. Read and annotate article in Highlights on iPad
  2. Readwise ? somehow will get those highlights? and then I can export to Markdown?


For 3 please try out Zotfile plugin for Zotero. All attachments can be moved into a folder inside iCloud/wherever you want it. Best part, Zotero remembers where it is and when you open (double-click) on your reference, you can choose to open with the PDF reader app of choice.

For viewing/annotation pdfs, I use PDFExpert across all my devices. Works well :+1:

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Agree with @noddyvinod on Zotfile plugin to ranmea nd handle the attachments or PDFs.

It has a send to tablet and get back from tablet. I use mdnotes to ge thet markdown notes out of zotero and then I can brig them into Obsidian directly.

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Not sure if your on the Zotero beta, but it now supports direct export of highlights to markdown format on Mac. The iOS beta is closed, but does not have this function yet. The iOS app does sync to the Mac however, where you can then export the highlights.

I’m very interested. BTW, this article may be of interest:

This is probably not all that you want but it is easier for those of us less technically trained. PDF Expert will export annotations to Markdown very easily. I have this setup to export to Markdown and open in Drafts. From there I can save to my Obsidian research vault.

Highlight annotation in PDF Expert:

Exporting Highlight to Markdown from PDF Expert:

Result in Drafts:
NOTE: Obviously one can skip the Drafts step and save directly to any folder or fault.

Final “Product” in Obsidian: