Best tools for organizing PDFs in Obsidian

There are many tools for organizing PDFs in Obsidian, but which one is the best? In this video, I go through several options, including DevonThink, Readwise, Skim, and Zotero. For my (non-academic) use case of organizing my TTRPG-related PDFs, I decided on Zotero-- but maybe something else will be better for you!

// TIMESTAMPS
00:00 Intro
01:03 My requirements and criteria for a PDF organization tool
03:30 Option 1 - Obsidian
06:06 Option 2 - DevonThink
08:23 Option 3 - Readwise
10:28 Option 4 - macOS + Skim
13:35 Option 5 - Zotero
14:17 Categorize: Installing plugins in Zotero
17:06 Process: Annotating in Zotero and exporting to Obsidian
18:40 Reference: Deep linking in Zotero
21:46 Save: Linked files instead of stored files in Zotero
24:13 Share: Changing the linked attachment base directory in Zotero
25:30 Example - Processing Arcadia PDFs in Obsidian

// RESOURCES

Tools

Zotero plugins mentioned

Thanks to the following people for their input and help in experimenting:
- @argentum#3920 on Discord

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// ABOUT ME

// APPS I USE

// GEAR

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[nicolevdh]

This was a long one, but I wanted to be thorough! Use the timestamps to jump around, and check the description for links to tools I mentioned. I also want to call out something about the Zotero deep link format.
The Zotero link should be in one of the two formats to be clickable from within Obsidian:
- OR
-

While experimenting, I found that only the first worked for me, but oddly, the second worked better for friends and we couldn't figure out why. Try both!

Obsidian plugins used: Dataview, Templater

[SeanMassa]

This is one of the best comparison reviews on youtube. I'm sure this took a lot of work. Great job!

[maks_st]

I had this question of how to process PDFs in Obsidian. I now realise that Readwise is the best option for my needs, so far at least. Thank you for the detailed overview, Nicole!

[Trecoolerok]

This video was the reason i switched to zotero. I also have a huge collection of pdfs inside complex folder system, and adding them manually would be hell. Though I find more smooth way to export highlights to obsidian with obsidian-zotero plugin and biblex addon in zotero. It automatically add links, so you don’t have to manually edit links. There is one problem though. Pdf drawings on pdf inside zotero app on iPad doesn’t exports. Though I think there is the way to get these drawings outside exported pdf - because ipad software can manipulate with these drawings - so there must be the way to extract them, and export, let’s say, to excalidraw. So thanks again for this marvellous video!

[tejav]

You are awesome, Nicole. Keep up the great work. You helped me a lot in my Obsidian choices.

[hydroross]

Regarding DEVONthink I’ve been very successful and satisfied with “indexing” my Obsidian vault folder. DT has good built-in Markdown-friendly annotation features with backlinks to the original PDF. After annotation/note-taking, I save the annotation markdown file into the Obsidian folder and archive the PDF separately. Works great. On the other hand you are spot on regarding slow and fiddly cloud syncing with the iOS app. Nicole, thanks for the excellent video. Your efforts are much appreciated.

[davidwgilmore]

Great review Nicole! I've also started using Zotero as my Read It Later library. I put everything in there - YouTube videos, podcasts, PDFs, articles from the web - and since I can tag it all I have all of my references in one place

[KenoticMuse]

I think your take on Devonthink is very fair. I'm a fan of Devonthink, but I don't use it across multiple computers, so it's pretty much local only, and I have a use case for it.

[davidgrubba]

Hi, thank you so much for the video. My only suggestion is to use the Zotero plugin integration in Obsidian; this would make the task much easier.

[MarkLevison]

Nicole - I agree that for you Zotero is a great choice. I think you did DEVONThink a disservice. I use DT on a daily basis. Once configured, the sync over Dropbox is rock solid. My archive is 1/3 the size of yours and it’s been working flawlessly for over a year. The killer feature of DT that you missed is search. Hands down it is the best I’ve ever used. So it wasn’t for you, but I don’t think you did it justice in your comments.

[ThomasTrutt-oi]

thank you for your videos. I just started moving all my notes to Obsidian and have been binging your videos..

[visciuti]

Adoro seus vídeos! Este é exatamente o que eu estava procurando para pdf de artigos científicos! <<Respondendo em pt-br depois de ver a sua template do Obsidian =)>>

[Anglosphere-uihv]

I use obsidian and pdf++, to classify i simple do an index note and drags books related to that note subject, not as much flexible as tagging ...but i have no need for that i dont handle too many gb of pdfs so i guess those index notes are more than enough for me, its like library reference cards after all. You could also to a note per pdf as a note registry and add tags to it, it would work for your data view and direct access to the book. And you do everthing inside obsidian of course if pdf++ annotation is enough

[adriancabezas]

I really like Obsidian, but I tend to use Evernote because I haven't committed to personalizing my vault. For now, I'll continue to watch videos of people doing cool things with their vaults and live vicariously through YouTubers. Keep up the good work! Your videos stand out above the other Obsidian videos I've seen.

[fabiankeller]

Thanks for the detailed comparison, much appreciated!

A question on Zotero: What happens if you rename or move the PDF files in our Dropbox folder? Will the Zotero links be broken, or is there some sort of re-index so that it can re-discover the PDFs under their new path?

[brunoresendesantos]

Simply amazing. Been looking for something like this for ages!

Great video.

[fafilingdo]

I have a question, when you configure zotero to your online drive, do you put it in the same folder as your Obsidian vault or a different folder?

[uryaar]

Great video! I just started using Zotero for academics in order to use the tagging system as well, and still trying to figure out how to merge it better with Obsidian. This gives me some good ideas!

[gideon]

Why not just use Obsidian Zotero plugin? It has most of the functionalities you mentioned

[ZakirHussainIbrahim]

Hi Nicole. Great video. Is there a work around for Mendeley instead of Zotero? Thank you in advance.