# [[Best tools for organizing PDFs in Obsidian]] plugins:: "[[Zotero]], [[Skim]], [[DevonThink]], [[Readwise]]" <iframe width="560" height="315" src="https://www.youtube.com/embed/VqOc9OsMX_s" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> ## Timestamps [00:00](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=0s) Intro [01:03](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=63s) My requirements and criteria for a PDF organization tool [03:30](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=210s) Option 1 - Obsidian [06:06](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=366s) Option 2 - DevonThink [08:23](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=503s) Option 3 - Readwise [10:28](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=628s) Option 4 - macOS + Skim [13:35](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=815s) Option 5 - Zotero [14:17](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=857s) Categorize: Installing plugins in Zotero [17:06](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=1026s) Process: Annotating in Zotero and exporting to Obsidian [18:40](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=1120s) Reference: Deep linking in Zotero [21:46](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=1306s) Save: Linked files instead of stored files in Zotero [24:13](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=1453s) Share: Changing the linked attachment base directory in Zotero [25:30](https://www.youtube.com/watch?v=VqOc9OsMX_s&t=1530s) Example - Processing Arcadia PDFs in Obsidian ## Transcript - Most of the books that I read, both fictional and nonfictional, are either in .mobi or .epub format, which means I can read them with a Kindle or a Kobo ebook reader. Now I already have workflows in place to get highlights from those places and into Obsidian, but there's one glaring gap in my system, PDFs, and somehow I've ended up with a lot of PDFs, a 127 gigabytes of PDFs to be precise. Most of them role playing game related. Now the problem with PDFs and in particular RPG PDFs is that they're part reference and part fiction, so they're not really the sort of things that I want to highlight in the same way, which means that they easily fall through the cracks of this entire process. In this video, I'm gonna show you all of the options that I tried out to make some sense of this PDF mess, the option that I did choose and why I chose it and how to set it up to work with Obsidian. Spoiler alert: it's Zotero. First, let's talk about my requirements. My use case isn't academic. I don't really care about citations. I only vaguely care about being able to highlight. I care more about other things like being able to deep link and tagging the PDF so that I can find the ones that I want. This is a depiction of the things that I'm looking for, in Canvas. When I have a PDF, I'm going to want to be able to do five things with it, and these are the criteria that I'm going to be judging the options on. So I want to be able to categorize, process, reference, save and share them. Categorize, to me, means being able to tag the PDFs, so I wanna know whether it has character options or adventures or it has a bestiary and I also want to be able to query them later in Dataview. Now I will settle for some sort of querying or search system in another app, but I just think it would be really cool to be able to do it in Obsidian since that's where a lot of my notes are already. I wanna be able to process them, which means I want somewhere where I can still read them like on my phone or something and that doesn't screw up stuff and be able to annotate, meaning highlight or take notes on the PDF itself and then bring those ideally into Obsidian. I want to be able to reference them, which means two things for me. One, I want to be able to have deep links to a specific page within Obsidian. So I wanna click on a link in Obsidian and the PDF opens up at that page and that way I can construct a sort of table of contents. Then I wanna be able to save copies of all of my PDFs both locally and on the cloud. With 127 gigabytes of PDFs, I'm not going to want to store everything locally. Some of it I'm going to be keeping on the cloud, namely Dropbox. And I wanna be able to share my PDFs, both sync them across multiple devices, I have a smattering of laptops, some of them are macOS as my main operating system, but I do have some Linux ones and I have an iPad and an Android phone that I use a lot. Ideally, I'd also like some sort of way to be able to share them with others, especially people that I play games with. There are few options that I wanted to explore. The first one is just doing everything within Obsidian because I already use Obsidian pretty heavily, but there are some things that it doesn't do. For example, you can't easily categorize PDFs. Even if you have them in your vault Obsidian isn't going to be able to tag it because it's not a markdown note. You could kind of do something with Excalidraw, but it's not ideal. So it gets a big cross for me there. It also gets a cross on processing. I believe that there are some plugins that can do this within Obsidian, but it's still not great and just the reading and annotation process is not robust enough, so that's a cross for me as well. On the reference front, Obsidian actually does pretty well in this regard. So let's say I have a new note and I already have a PDF that's within this vault, so I'm going to put in the title for it and it is an asset, so normally I would click on this and I would be able to open it and let's do that now. So when I open that up, it's dismantling cognitive biases. This is a very old one. So let's say it's 70 pages because it was doing animations. So let's say I want to go to this slide, so it's number 10, so let's close that. All I need to do is go here and then put a hash and then I wanted to go to page 10. So now when I click on it and I say open it in a new tab, it's gonna go right to the specific page. This is what I call deep linking, and the cool thing is if I put all of my PDFs in Obsidian, that actually works pretty well. So it's a tick for Obsidian on reference. Obsidian gets a tick for local because it does store everything locally and it doesn't really matter whether you also back that up or sync it to the cloud, so tick for that as well. I've also been able to share Obsidian vaults through Dropbox with other people and even GitHub at work. So that's a tick as well as long as the PDFs aren't, you know, a 137 gigabytes worth. So, you know, I think that is a pretty extreme case. I think for most people this is gonna be a tick. The cons for Obsidian other than the size limitations are the limited PDF features. You kind of need some sort of plugin to be able to annotate from the PDFs at all and even just to improve the PDF reading experience. The second option is DevonThink. I first heard about DevonThink from my friend Leah Ferguson who uses it quite extensively, but let's see how it does on the rubric that I have come up with. It gets a tick for categorization because you can tag things on DevonThink. You can also do deep links on DevonThink, so it's a tick for that, and it does really well when everything is local. Unfortunately, that's where things start to fall apart for DevonThink, at least for this particular use case. On the processing side, you can't really annotate something in DevonThink and then expect to bring that into Obsidian. I didn't find a way to do it, really. Let me know if you do have a way. I also got a lot of errors when I stored my files on Dropbox or iCloud. For those who don't know, you can kind of make it so that some files are available online only and I expected that I'd be able to do that with some files, but DevonThink threw up a lot of errors because it was constantly checking the state of the files and I had to like re-index them and that wouldn't find them and there were errors and it was just really a pain. It became pretty clear that if I was gonna use DevonThink then everything would have to be local all the time, which isn't really feasible. I use all of my PDFs in different devices and they don't all have a lot of storage space. I also tried to install DevonThink on two different computers and trying to sync them up was such a pain. They have this, their own like little system and I don't know what I was doing wrong, but I just was so frustrated trying to get it to work. It took so long and I still didn't get it to work. And in terms of syncing it across devices, DevonThink to go, which is kind of the mobile app, is iOS only. So it's only good for my iPad and my main mobile is an Android phone, so that was never gonna work. Other cons for DevonThink are that I just found it really bloated, and by the way, it is expensive. You have to pay for it and depending on what you choose, it could be significantly expensive for what you get, unfortunately. Another option that I considered was Readwise, because I love Readwise. Readwise.io/nicole if you haven't tried it, but this isn't really the sort of thing that Readwise is excellent at. So I'm putting it here because it was one of the things that I tried, but it didn't work out very well and I don't think that that's the fault of Readwise. Readwise was never supposed to be a repository for PDFs. They do have a preliminary support for PDFs though, which is why it still made the options list. It was particularly good at processing, probably the best out of all of the solutions with one exception maybe. And that's because on Readwise you can highlight and there's already a Readwise to Obsidian official plugin that brings in those highlights. I really like that and I already use it in other workflows, so being able to do it with PDFs would've been pretty cool. It also gets a tick on the cloud front because Readwise is a SaaS platform, so everything is stored on their cloud, which means it gets a cross in everything else. Readwise fails on the tags front because there isn't really a way to add tags to the PDF itself. So if you go into Readwise Reader, there's no way to add to this. Like, it would be nice if you could change the category, but it's read only for now, although they do say it's coming soon. Readwise also doesn't give you deep links to the PDFs. At best, it'll give you a location, which has never really worked well for me. It doesn't take you directly to the PDF in any case. It isn't local, it is cloud only. It is a SaaS platform, so you could argue that it's a little unfair to add it here. It is also not great for sharing. You can share your highlights to Obsidian and then share your Obsidian notes, but that's kind of a workaround. This isn't really Readwise's forte. Another solution that I heard about from my friend Andy Polaine, is the combination of macOS and a lightweight app called Skim, which I quite like. Skim is an open source PDF Reader that is really easy to use actually, and being able to use it with macOS means that this is probably the simplest solution. Categorize is a yes because you can use macOS's innate file tagging system to just be able to assign colors to certain files and be able to search them through macOS. For processing, Skim does actually let you highlight and annotate stuff, and it also gives you deep links, so they're not entirely compatible with DevonThink ones, but you know, if you have the page number, you can kind of do a find and search and replace to get rid of the rest and put them into the format that you want. Actually, let me show you that now, since I do have Skim. So this is Skim, this is a PDF that I opened with it. And let's say that we want to open to this page where all the cards are. In Skim, I would just go to edit and then copy url. And then in Obsidian, if I just paste something, this is what it looks like, and this is what's called a deep link. So if I put parenthesis on that and then I make a link here, I can make it like a markdown link. And then when I click on it, well let's close Skim first. So I'll close that. Skim is now not open and I'm going to click on it. It says, are you sure you wanna open this link? And then you can click on that. And it took me exactly to the place where I did the copying of the url. So that actually works pretty great and it's so lightweight and quick that I really wanted to like this. Where it starts to fall down is that it is local only. It's pretty rudimentary. Doesn't really have a robust collection system or anything, and it doesn't remember things about something you've put on the cloud. So it's either there or it's not going to be able to see anything, any of the PDFs that you've got marked as online only on Dropbox, let's say. So it's a cross for cloud and you can't really share stuff. So if you highlight stuff from it, if you do tags, tags are really hard to share. I think that Andy said that you could do it through iCloud. Well, I don't use iCloud and I want to be able to share it with other people who use a variety of things. And for that, I don't think that it is the most futureproof. The main con of this combination is that you're tied to a macOS. While macOS is my OS of choice right now, I don't feel good about tying myself down or committing to a specific OS. And then what happens if I switch to Linux? Well then I'm just going to have to re-tag everything? Not acceptable. So it wasn't good enough for me. Finally, we've gotten to the last option and thankfully it worked. I mean, maybe there are other options. If so, leave them in the comments below. I kind of just stopped here because I was just so happy that I found something that ticked all of my boxes. It is Zotero. So let me show you how it ticks all the boxes. Zotero is an open source app, and I have already put in a bunch of all of my RPG and RPG aid stuff and I've got PDFs in here already, so I can make different libraries, I can make new collections. I can group separate PDFs into one book. So there's actually a lot of room for being able to organize my stuff. Zotero takes the categorized box because I can go into the PDF here, so I can go down here. Let me just remove myself for a second so I can show you and I can add character options and then I'll put items and also spells because there's some tattoos where you can, they kind of let you do some spells. Here's the big asterisk for Zotero. I still think it comes the closest to what I wanted to do. However, that is at the expense of plug-ins, not Obsidian plug-ins, Zotero plug-ins. So right now, I've got two plug-ins that I think you need. The first is the Zotero folder import. I'm gonna put the links to these plug-ins in the description below so that you can do it too. So this is what a Zotero plug-in looks like on GitHub. They are written in type script. You download the XPI by clicking on it here, and then when you go to Zotero, you would go into tools and then add-ons and you can click on the wheel here and click install add-on from file. Then you have to select that xpi. And you may have to restart Zotero. You're gonna have to do this I think for at least Zutilo and folder import for Zotero. So the Folder import is really awesome because otherwise you're gonna have to do this manually, which really sucks. I wouldn't, I tried to do that. And luckily, Argentum from the Obsidian Discord told me that there was a better way, and I'm super grateful to her for that. I might demonstrate that in a little bit. The other plug-in, Zutilo, which is, utilo is actually an Esperanto word for like a tool, but if you go here, then you can, once you've right clicked on the PDF, you can click copy tags to clipboard. And now you have the tags that you have set here. So, let's say I'm in Obsidian, I'm just going to paste it here. Now I have the tags. So now there's an easy way to get stuff out of Zotero and into Obsidian. So the way that I'm sort of looking at this is by using Obsidian as kind of like the main Database, it's going to be much more future proof because I'm gonna be able to view it on all devices, on all operating systems. It's still just gonna be a markdown table so even if Obsidian goes away, I can still open it up in a text editor. And if I really need to I can write a script to parse all of the data and then send it to like an actual Database if I wanted to do that. That's a tick for categorize. Processing is also pretty good. Like I said, this isn't a huge deal, but you can also add stuff to Obsidian this way. So you can sort of select parts of it and then you can add comments. And then you can also like add sticky notes. Here, chained tattoo. So if you want to put these into Obsidian, you're going to have to go back here and unfortunately install another plug-in. This time, it's gonna be called Mdnotes. Again, link in the description for how to get it, but you would first create a note from the annotations. Then I'm going to add both of these to a book because it both belong to Tome of Mystical Tattoos and then I'll put both of them in here. Now I can click on the Tome of Mystical Tattoos kind of book that I made and then click on Mdnotes and export to markdown, and it'll ask me where I want to save it. And I'm just going to select that folder. And then when I go into Obsidian, there's a Tone of Mystical Tattoos here, and when I click on it, it has the tags. These are things that you can assign in the template as well. So I had these tags to be set. These aren't the ones that come from Zotero, but you can set that as well. This is because I haven't really messed with it too much because I don't really find it that useful. I just like to know that if I wanted to, I could. So that's how to process stuff in Zotero. So the third one is reference. Zotero nails that actually, but for some reason it's not an advertised thing and it's not in the core functionality of the app, which I don't get. But anyway, it is in Zutilo. So here's what you gotta do. You have to go into tools and then Zutilo preferences. So I suggest that you tick the radio button for Zotero context menu for copy select item links, and then also go to shortcuts. This is the way that I use. And then for copy select item links, you can create some sort of keyboard shortcut. Now this is the one that I created, and then you can apply it. So now, when you go here and click on Tome of Mystical Tattoos, I'm going to use my keyboard shortcut and then go into Obsidian and I'll show you what that does. This is what it now looks like. This looks very similar to the Skim link. So I'm going to put Skim here just so you know what it looks like. So, it's just that it has Zotero at the start here. However, the problem is if I put a Zotero link here and then I turn this into a markdown link, if I click on it, it's just going to take me to where that book is. It's not actually going to open it yet. I had to figure this out for myself by Googling, there's actually a specific syntax that you can use. I'm using a keyboard shortcut using a tool called Espanso. Different video, but this is what it needs to look like. So, what I'm gonna do is I'm gonna copy this unique identifier for the book and I'm going to replace that. So now I'm going to call this the Zotero select link because it's a little bit different. And then this is the Zotero, I'm just gonna call it PDF link. So now if I click on that, it opens up the PDF. Now the problem is it's still not going to where we want it to go, so we need to get the actual page that we wanted. It is actually page 136 just because of PDF reasons. So I'm gonna go back here and then I'm going to put 136, and let's go back and like just scroll down a little bit so it's a bit different, it's in a different place. And then in Obsidian, I'm gonna click the PDF link. It should take us to page 132, 136, which it has. And this is back to the chained tattoo. So in this way, you can actually be able to click on links in Obsidian and go straight into the place that you want to be at. So it is a huge yes for reference material, and I'll show you how I put everything together later. Right now, I'm just going through the things that Zotero does well. On local and cloud, Zotero does really well. It's a thumbs up for both because it does well when files are stored locally and when some of them are stored like online on a cloud service. However, to be able to have that seamless integration, I do recommend that you choose linked files instead of stored files. Stored files are the normal kinds of files where when you put them into Zotero, you are importing them into the specific folder that Zotero has chosen. However, I prefer to use the linked files so that Zotero itself is not adding anymore bulk. That's not doubling up on storage space, it's just using, it's just pointing to files that already exist elsewhere in your system. Before you get too far into importing PDFs into the Zotero, go ahead and go to Zotero, and then settings and under linked attachment base directory, there's a base directory here that you can choose. Now, you might need to change this. So go ahead and change that file path to the folder where your files are actually going to be stored. So in my case, it's my Dropbox folder. When you go to my library with that plugin installed for folder importing, first click into the folder that you want to start importing into, and then you can click this plus icon and then add files from folder. So I'm gonna go into RPGs because I know that there's a new RPG that I bought that I haven't put in here yet, and it is called Star Crossed. So I'm going to open that one and it's going to ask you, in this case there's only PDFs otherwise it would ask me for which types of files I would want to import into Zotero. And importantly, I'm going to select link to files rather than store copy of files, just to save space, like I said. Then click okay, and now it's importing those PDFs. Now I'm actually going to create a new sub collection for them called Star Crossed, and then I'm going to move these into the Star Crossed collection. So now they're in the Star Crossed collection. And if you can see that little link icon, that means that it hasn't been duplicated. It is still pointing to a Folder on Dropbox where I've kept these PDFs. Now remember when we set that base directory to the Dropbox directory, well, we can now go back into that. And if we wanted to change this, like for example, we're on a new computer now, but that computer is still syncing through Dropbox, maybe some of the file paths are different. Well, you can go ahead and choose the base directory, select the new directory, and it's all going to work. I've verified this on another computer with slightly different paths, as long as it's the same set of files, and it's just a matter of pointing to where it is. All of the links, because they're links and they're not storing the actual copy are going to work, and so are the tags and you know the collections that you've got and everything like that. So that is actually pretty awesome. So if you are keeping score, Zotero ticked all of the boxes, and really the only cons are that it is a little bit janky. There are some things that aren't quite as smooth as I would like. And the other con is that you do need plug-ins, Zotero plugins, however they are free, and Zotero is a free and open source tool. So I think it can be forgiven based on all of the ticks that it's got. Now I'm gonna show you how I've started to use the system in Obsidian. I really like MCDM's Arcadia magazine, and I started to create a note per Arcadia edition. Arcadia's really awesome because they usually have three or four different sections written by different people, and they're entirely different articles with ideas for how to improve your D and D 5E game. So what I'm doing here is I have the source Zotero link and a link to these pages, but I'm also tagging each adventure, and I'll show you how that comes into play later. So then when I click on Power Is Where You Take It, it automatically opens up in Zotero to that specific page. So that's already really cool, kind of like the table of contents part that I was showing you. But the really cool thing is, because I did this for all Arcadia things, except I saw there was one that just came out, I haven't done it for that one yet, but in Dataview queries, I am now able to have this pretty simple query that just brings in everything with a file name Arcadia, and shows the author, the tags and the description. So now this is returning what I've got for all of the Arcadia stuff, all of the section headings and what they are. So, because they're tagged now, I can, for example, click on rules, and now that brings up, because it's just an Obsidian tag, it brings up everywhere where I have rules. Now I think this is only Arcadia that I have this tag on, so it's only showing Arcadia stuff, but now I can see like, "Hey, this parentage and upbringing section from Arcadia 22 had character options and rules." So then I can click on that. Parentage and upbringing looks interesting so I'll click on that, and now I'm on that page of the PDF of that section of that volume. I mean, how awesome is that? I'm super excited about this because now those PDFs aren't just languishing in some forgotten folder of my operating system. You know, I'm actually going to be able to use these PDFs and call them up when I need to. I've known about Zotera for a while, but I'd only ever considered using it in academic contexts. Turns out it's pretty good for non-academic PDFs as well, especially when used in conjunction with Obsidian. Thank you to my friends, Andy Polaine, Leah Ferguson, and Argentum for letting me pick their brains about various tools and really helping me on this process. Thank you also to the fine folks on my Patreon only Discord server in the TTRPG's channel who gave me the push I needed to finally make this video because, yeah, I've been thinking about this for a while. If you'd like to see more about how I get the most out of these RPG PDFs, then check out this video where I go through my DM's brain attic in Obsidian about how I start to pull things from these various PDFs. Thank you for watching. Now I gotta go and make TOCs for the rest of my books, the things I'll do for games.