iPad reference manager help and suggestions

Looking for help in reference managers. I look through multiple medical journals with BrowZine through my institution which is great for aggregation, and then send to my reference manager on iPad. I have been using PaperShip app on iPad (through mendeley). The desktop mendeley app has limitations in flattening annotations, so playing around with Zotero beta and considering moving to Zotero with PaperShip instead. Seems decent but limited in storage. Tried bookends and didn’t have great luck. Endnote I own so have a ton of storage but the iPad app is horrible, borderline unusable and clunky for annotation. I have not found an easy way to export from a reference manager and edit on PDF expert and then send back to reference manager without duplicates (if there is a workflow please let me know!)

With all of the great ideas in the forums and podcasts, would like to get my annotations out of reference manager to text file to summarize/reference later, set up a zettlekasten etc. I am having issues achieving this. Sending to PDF expert gets me close, but only sends out annotation as PDF file. Sending it to highlights app puts it as html annotation output.

Is there an easy workflow on iPad to go from reference manager out to text? Would love basic text I can put in obsidian, OneNote, or apple notes depending on content.

Thanks as always to this group for help and idea.

Edit: I should mention I see highlights may be able to do this, but I’m not sure it’s worth the cost to just move annotations as I no longer write academic works just stay up to date with literature. I would just copy and paste for my use case if needed or keep taking handwritten notes in OneNote to summarize my annotations when I review.

Look here for the recent and ongoing thread(s) here from @DrJJWMac who is working through developing an approach for a similar requirement for tracking annotations and notes on technical material.

Thanks. That looks a bit to complex and requires highlights paid. I can probably just pay for highlights, export from any ref manager and then use highlights export to text I assume for that functionality.

From the app Highlights …

  • When the annotations are only highlights of text, you can export in markdown format. You can do this from iPadOS or macOS.

  • When the annotations include pictures, you must export as a textbundle. Doing so from iPadOS creates a package folder rather than a regular folder with a file extension. Converting the former (iPadOS) requires an extra step.

In my experience on the iPad, nothing yet beats Bookends for overall feature set, stability, and inter-operability. ReadCube Papers is a close second for its intuitive and fluid workflow, although they have yet to offer an annotation tool to capture figures, their annotation tools are clunky to use by comparison to Bookends, and their share sheet option fails to work. I dare say that I abandoned PaperShip on the iPad years ago as being rather limited and limiting.

On macOS, I find that working with Zotero as a PDF reference manager/citation manager is not at all intuitive, fluid, and easy. After working with Bookends and ReadCube Papers, going to Zotero is like moving from a 12 speed bicycle to a one-speed unicycle–yes, it can go in that direction, but you have to do your own balancing acts to get to the same places (if at all). Some folks swear by Zotero especially as a counter to the occasional difficulties or non-intuitive approaches that arise in Bookends (and I’ve faced my share) and/or as a reasoned counter to the publisher-owned associations faced when using either ReadCube Papers, Mendeley, or EndNote (and I discount these concerns because the apps all work very well in their own ways).

Hope this helps with further insights.


Can you expand on what you feel makes bookends better for annotation on iPad. I find PaperShip does an excellent job and works well. Previously the mendeley app before shut down, and now the zotero beta app work well. Endnote annotation I don’t enjoy, it’s fine to highlight but doesn’t make use of the Apple Pencil.

I will admit to only spending limited time with bookends however so would like your opinion as someone who seems to use it more frequently.

Thank you

I cannot speak to PaperShip. It may be worse, the same, or better than Bookends for annotation. The reason that I stay with Bookends iPadOS are

  • Bookends integrates well with Highlights and Devonthink (the latter is more important than the former to me).
  • I can split my expansive citation library into smaller pieces using Bookends macOS and sync only those sub-sets to Bookends iPadOS.

I am evaluating ReadCube Papers as the only other option. The app is doing a good job on both the macOS and iPadOS platforms, with the exceptions that I noted. In addition, ReadCube Papers will offer me the opportunity to share with my research team who use Windows systems. In effect, if ReadCube Papers becomes on par with what I can do with Bookends right now, I may be on a knife’s edge to jump ship.

Overall, which ever iPadOS citation manager you use (since this seems to be your main point of entree to the annotation process), if your end goal is to move annotations to Obsidian, you will need to pay attention to the two possible formats, markdown or textbundle, and you will (almost certainly) have to do the heavy lifting (moving the annotations out of the PDFs to markdown to Obsidian) on macOS.


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I also use Bookend on iPad and am quite happy with it. It is easy to markup with the pencil, and I like that the iCloud folder is available across devices and easily indexed by Devonthink. I use a shortcut to get annotations out to drafts (and to “bump” the page numbers if needed), where they are easy to work with before dumping into Obsidian as cleaned up notes. (A really simple action does that — I am using an earlier iteration of this one → Obsidian — OlivierPS | Drafts Directory). I find it a really smooth workflow. A few screenshots below. @DrJJWMac I believe works with moving images into Obsidian in his workflow — I tend to do this less often, but another simple shortcut saves screenshots to my obsidian media folder. I can do this entirely on iOS.


This looks like it may be a solution. I’m thinking maybe I use whatever ref manager I want, with an export to highlights since I can then export and “copy” and paste into onenote, obsidian, or Apple notes. (I just bought highlights to mess with). Seems like making a shortcut to take the copied text and paste into a note would work for obsidian or Apple notes….onenote jus requires copy paste.

Now to learn some shortcuts……

Part of my problem with highlights is that I like to mark up with the pencil in the margins. (I dream of a day that this marginalia can be ocr’d and exported.

I understand. I love onenote for annotation and organizing. In grad school everything was pdf and PowerPoint I sent to onenote and used the old school convertible Wacom powered tablet pc to annotate, so much of my workflow is still in onenote. I know I’m the minority, but I do love onenote. I still keep my work notes and follow literature in it.

I think I am hearing about these other systems and trying to fit a square peg into round hole….but getting to just text to input is definitely something I could make use of.

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I’m sure this is not the most elegant way to do this, but I think you have set me on the path of something free that works for my use case.

I’m annotating pdf in whatever app I want….when I want to export text I’m exporting to highlights, and then do a notes only export to pdf (which is free), and use a shortcut to take the pdf and convert to text and paste to the clipboard. Easy enough for my use to put into onenote and keep using it for now.

I’m sure I can get more complicated and have it go to multiple places/notes etc but for now it’s all I need.

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Great - but I guess I don’t understand why you are including highlights, when a shortcut like mine above can take it directly to the clipboard from PDFExpert, Bookends, etc. Or is that your PDF annotation tool of choice doesn’t allow exporting of your annotations (which is weird!)

Both PaperShip and zotero on iPad export the entire pdf, not just the annotations………so yea I need to change to another program and do straight export (need to pay for another subscription), or can add the step to go to highlights just when I want to pull out the annotations only.

This isn’t something I do often so can’t really justify the cost to switch from my current app that works for free.

Edit: doesn’t pdf expert still export the whole pdf page where there is annotations? Or will it only export the highlights?

If you click on the annotations, you can then just export the annotations (it will do so as a pdf, but the shortcut above will convert it effectively).
If you are using zotero, you really might want to look into the extensive plug-ins available through Obsidian. Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow - Share & showcase - Obsidian Forum
This may seem overwhelming, but lots of folks on the discord channel can walk you through it.

Thanks. The pdf expert export free version goes to html, which should be even easier to make a share sheet extension to go to text.

And I have looked through obsidian pages and it is all overwhelming……but my primary goal has been to use my current setup and get text to onenote and not learn a new app and not pay for more subscriptions……so it seems like the once or twice a week an export from my preferred reference manager to pdf expert or highlights and then share sheet once it’s txt works well enough for my use case.


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Great - sorry, I misunderstood and thought you were already using Obsidian. Good luck and enjoy!

Thank you. I appreciate the help, had been looking for a solution all in one to get the text out and hadn’t even considered a simple shortcut until I saw yours. A few little formatting issues are no problem to clean up.

But yes I basically want zotfile for iPad.

Amazing how such a small thing might be able to change a workflow.

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As a follow up, I have just come off this workflow experience on the iPad:

  • Open a PDF in Bookends to annotate
  • Put a split view window beside the Bookends view (in my case, I used GeoGebra to create a graph of a function in the PDF so that I could see how the function behaved over a region of space)
  • Share out the split view window to COPY it (i.e. put an image of the split view window onto the iPad pasteboard)
  • Hold+select a position on the PDF in Bookends and select paste
    → the image is pasted on the page

The image can be repositioned and resized. I added a note to the image. I expect the image + note will appear in the .textbundle(markdown) export when I bring the PDF to Bookends/macOS and on to Obsidian.

In summary, you have need to create shortcuts to capture images into PDFs using Bookends iPadOS.