What are the best tools for annotating and then extracting notes from PDFs for academic writing

I am looking for advice specifically from academic writers regarding the best tools for annotating and then extracting notes from PDFs to then be used in my wrting. I have been using Acrobat but it is just basic and not really satisfactory. I was not satisfied with how BookEnds handles notes.

I have come across

MarginNote marginnote.com


LiquidText liquidtext.net.

They both look intriguing and powerful but the former has very little English documentation or tutorials and seems aimed at the Chinese market. Have not yet kicked the tires of the latter so don’t know yet if it would be easier to learn.

Anyone has experience with these or any other solutions that they can recommend?

I use Papers 3 to both collect, read and annotate scientific articles. I then export the reference and annotations to a .txt file using an Apple script provided by the developer, import that as notes in Scapple if I need to play around with the structure, or import and split into Scrivener so each reference becomes its own entry in the Research part of the Binder.

I’m not sure if you can get the standalone non-subscription version of Papers e anymore, but that’s my way of doing it.

When I first came across MarginNote and LiquidText I allowed myself to be seduced by the look of them, paid my money, and then hardly used them. There is one big problem with both of them (for my working method) and that is getting information out of them and into another program. Other software is much better at this, and I have ended up using (mostly) PDF Expert and Highlights (version 1, as I am still on Mojave). I like Highlights a lot, as it creates a Markdown version of your highlighted sections, which it is easy to transfer to another program. I use DEVONthink to store a lot of my material, and I have recently been using The Archive for notes, though I am beginning to use Tinderbox a lot more. It’s all a bit of a mixture at the moment, because DEVONthink’s update to version 3 broke some of my working methods, and I have only just gone back to it now that version 3.5 has made life better for me.

There are so many tools out there that it is pretty bewildering. I can only say that experience has taught me that to some extent what works for you will depend on the kind of work you do, as well as personal preference. One person’s solution is another person’s problem. And any sort of recommendation tells you almost as much about the person making the recommendation and the work they do as it does about the program they recommend. Ultimately, I believe that each of us has to carve out their own path, and that means trying stuff and seeing what works for us.

Best of luck with it.

PS: “academic writers” covers a LOT of different people with different needs. Those who write long history books once every three years are probably going to be doing different things from biologists who need to get articles out in rapid succession.

Thank you for your thoughts.

Thank you for your thoughts and insights from your experience.

Yes they are indeed seductive. I like the simple approach of Highlights but I am still using High Sierra (because of 32 bit issues) so I can’t use it )-: I will be getting a new MBP so will have an opportunity then to use Highlights.

Will play around more with MarginNotes and LiquidText to see if they can do what I need. Otherwise I will figure out a different workflow with Acrobat. I will look into PDF expert as well.

I have not been able t figure out how I would benefit from DevonThink so I uninstalled my copy. But obviously others do find it of value, I’m not one of them (yet).

I forgot to mention another possibility, which is Skim https://skim-app.sourceforge.io/.

It has not been updated in some time, but it is free, and it was certainly used by people working in academia (I was one of them) and was quite capable at the time. There was certainly no problem about getting information out of the application.

On other forums it has been observed that getting data out of MarginNote is a bit of a nightmare (that might have changed). But I would say that there is little worse than having one’s work trapped inside an application. Extremely frustrating.

Skim is great if you’re primarily working on a Mac as it uses its own annotations that predate native support for PDF annotations on Mac OS X. I’ve used it since 2005 or so. There’s a command line tool and robust AppleScript support to automate note conversion, extracting of notes, etc.

Lately I’ve mostly been using Highlights as I’ve been going back and forth between Mac and iOS a lot, and its annotations are native.

I use PDF-Exchange Editor

It will allow you to select text and copy or export it or paste it as text or rich text. In my set up it defaults to Microsoft Office directly but cut and past seems to work with anything. You can also make your selected text into a bookmark stored with the PDF and make many types of notes. You can also insert various types of notes into the PDF and optionally print them. This program is less expensive and more functional than Acrobat with only one exception. It does not have a good indexing filter (i.e. .pdx support for a group of files). So I still use Acrobat when I need to search a large pdf library,

Oh, if you get frustrated it also allows you to take a snapshot of part of the pdf. And despite what you may have heard about Latex, don’t waste a minute with it. It’s very archaic and fails miserably at most tasks. The last editor I considered a fully functional tool was put out by Digital Equipment and ran on a VAX. It disappeared when DEC was sold to HP. I doubt it will ever see the light of day again, and I’m not sure it was actually ever sold to customers.

Back on topic PDF-Exchange Editor will open hundreds of PDF files at the same time, and reload them all when you restart it. You can also save a project with all of the files as a workspace with a name, and reload the entire environment when you want to work on that project again. Its put out by Tracker Software.

Acrobat is an expensive has been. PDF-Exchange also does OCR and it has none of the memory management bugs that Adobe is famous for. I’ve used it since it was introduced. About twice a year I find something I need Acrobat for - usually searching a global index for a needle in a haystack - but even that function is being replaced by programs like File Locator Pro which can do several different types of searches and its very fast. I have one collection of approximately 1 Million documents in pdf format, and I can search all of them in just a few minutes. If you need the name search you can do it raw or from an index with good logical syntax. After getting close you can search inside the PDF’s for final selection. Naturally, everything must be OCR’d first.

I OCR with PDF-Exchange Editor mostly but Acrobat has a number of tools that make it better sometimes. Like OCR all files in a folder and/or subfolders at one time (sequentially). And you can still do other things with your computer.

The OP is on a Mac, though.

Then again, I’m not sure why this thread is in Using Scrivener …

You’re right. Moved. – Katherine

Sorry if I put it in the wrong thread. But since I saw threads about what kind of music people listened to while using Scrivener, or what fonts they used I thought to ask about this topic in “Using Scrivener” thread as I would be using it with Scrivener.

Thank you for moving it to an optimal location.

My workflow is messy, implying I could not find a satisfactory solution:

  • Papers for main long-term pdf library
  • Marginnote for mindmmaping and extracting information while crafting a manuscript
    -Goodnotes, mostly on the iPad + iPad, for proofreading, scribbling…
  • Currently looking for a Devonthink alternative, did not work me, that can help me to retrieve old annotations and non-hierchachical links-notes.

I tried Skim on a previously annotated text and it didn’t recognize any previous notes. Nor was it that intuitive. I may play around with it more later on a fresh document before deciding if I should delete it.

I use Highlights and like its features and user interface. I keep my papers (pdf’s in Bookends and Devonthink, but because the indexing is more robust in Devonthink that is usually where I go to find a pdf I’ve saved. I have set Highlights as my default for pdf’s, so double clicking opens the pdf in Highlights. I can then send a txt file of my notes/annotations to Devonthink for review, etc. I sometimes paste the file into Scrivener Scratchpad.

I’ve tried several of them, and have settled on Highlights for PDF annotations. The reason is because of the way it’s able to actually read pdfs, and will include spaces between words when lines of PDF text look like a single runon sentence. This was a big problem with Liquid Text and PDF Expert–their annotations would often result in runon words. And Liquid Text absolutely mangles ligatures.

So I store hundreds of pdfs of journal studies in DevonThink 3 (because of its superior search ability) and I annotate them using Highlights. Then… I move the annotations into Scrivener, which is where I do my actual writing.

So it might sound kind of anal, but I’m working on the 10th edition of a book that’s used in college courses, as well as having to create an online course that’s based on the book (thank you, Covid), and I find the workflow of using Highlights/Devonthink 3/Scrivener to be the sweet spot. During the shakedown process, I also tried using Bear, Ulysses, PDF Expert, Liquid Text and Evernote.

As for annotating web pages, I’m leaning toward using Liquid Text, but I wish they’d get their ligature act together.

I tried Liquid Text pro version on the Mac for annotating a web article and it crashed and lost the work I’d done. I then annotated the same article in Scrivener, and everything went well. So for now, I’ll be using Highlights to annotate PDFs and Scrivener for web pages and web articles.

(In all these years, I’ve never asked for my money back on an App I’ve purchased until now–Liquid Text on the Mac was quite a letdown.)

I concur. In my experience Marginnote is way better than LiquidText. The MindMaps are, in my opinion, quite valuable.