Mastering Essay Writing: Integrating Zotero and Obsidian for Seamless Workflow
Learn how to efficiently manage essay writing using Zotero and Obsidian. Discover tips for organizing sources, highlights, and notes to streamline your writing process.
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How I research and write in Obsidian
Added on 09/08/2024
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Speaker 1: Most how-to-write-an-essay videos that I've seen talk about the structure and the outline, so introduction, research, discussion, conclusion, all those sorts of things, but I don't see how they actually do it with the technology. Yes, they use Word and maybe a reference manager, but what is it that they're doing to get the highlighted points into the script? Because we think and we write and we write and we think. We sort of do it at the same time, and I've always been lost as to how other people have done it, so this is how I do it. I use Zotero as a reference manager, so it's basically a library of all of the sources, and you can see here I've got two sources at the top that I've added. I've got a citation key, which is like an ID for each of them, and it's done automatically inside of Zotero alongside all of the other information, so DOI, URL, authors, title, etc., and when I double click, it opens up a tab, and you can see I've already got some notes in here, and I can highlight, so I've got the pen up here, so I can highlight whatever words I want. If I change the color to, let's say, green, I can then highlight in a different color. They all appear in the sidebar, which I can navigate to quickly and easily, so that's a highlight manager essentially. You see I've got a post-it note there. I could just add a post-it note anywhere I want and add notes, so let's say adding a comment, so now I've got a comment on a green note in here. You can see I've added a comment and a tag to the highlight, so I can tag the highlight as well as add a comment to the highlight of my thoughts or ideas of whatever it is about this point, and as I scroll down, you can see I've got a table. I can come into here and then drag around. I don't want that to be green, so let's just change that highlight to yellow. Now I have a yellow highlight. I can navigate between the green highlights, the yellow highlights, or the tag. I can go between whatever I want inside of Zotero, but that's just getting the points. As I come back, I can then double click and open up another one, so let's just say I've got some highlighted points in here as well, but how do I bring all of these points into a place to write? I could go backwards and forwards between them, which obviously isn't ideal. I could copy and paste them into a Word doc, which is what I've done previously, but if I do a copy and paste, how do I get from Word, the copy and pasted text from Word, back to Zotero? Well, I'd need a link, and I don't want to have to manually make a link coming backwards and forwards, and I don't really want to come into here and then search for the file or the paper or whatever it is, and then try and find the highlight. That's just too much effort, to be honest. And when I'm working in Word, I used to have two different Word documents up, so I'd have a writing document and then a planning document, and the planning document would have tons of all these different notes sporadically put around, but I wouldn't have any order to them, because I read one article, then I read another article, and it was just a long list of a lot of points that I couldn't, like, puzzle piece put together. And for me, Obsidian solves those issues. So if I create a vault, it's basically a folder on my computer. I'm going to call it Essay Demo, and then I'm going to browse and find the external hard drive. Let's select Folder and then Create. So it's now created a folder called Essay Demo on my computer, and I have one file in it called Welcome. This is Obsidian. Going to my external hard drive, you can see Essay Demo. If I double click in, there's all of the setting files, and there's the actual file, the Welcome.md file. Now, if I was working in Word, I would have to have two or three different Word files up. If I change the name of this to Essay, and then let's add a new note and call it Source, you can see I've actually got two different files up at the same time split-screened, so I don't need to have to have two different Word documents open. And if I drag this in the middle, now I've got three, so I can have three documents open, or I could have multiple tabs, so multiple sources up on one side, and then my essay over on the other side. But before we get ahead of ourselves, let's actually bring in those highlights. So I'm going to go down to the Settings. Now, I personally prefer this to be Dark Mode, so I'm going to change this to Dark Mode. I'm going to go to Community Plugins, turn on Community Plugins, browse, type Zotero, Install, Enable, Options. I'm going to download the PDF utility, so it can read the PDFs. Make sure it's the Zotero database. Scroll down. I now want an import format, because I want to import highlights. I'm going to name it Danny Import. Now, Citation Key is what the file is going to be called. If we go back to Zotero, you can see we've got the two different items there, and they both have unique citation keys. I personally use, and would recommend using, an add-on called Better BibTeX for Zotero. If you search for Better BibTeX for Zotero, you'll find this page, and then we go to the Install Latest Release. Then we want to download the XPI. That's the most recent one. That was five days ago for me. Once it's downloaded it, I can then drag it into this window, and then it restarts Zotero, so it will update itself and say, hey, you've now got Better BibTeX for Zotero. So I've got my download here. I then drag it in, and it gives me the pop-up window. Obviously, I've done it, so I'm not going to say Install Now, because I've already got it there. Now when I go to Edit, I go to Preferences, I go to the Better BibTeX Preferences, and say open those preferences. I can then customize the citation key formula, and for me, I'd put the author, then the short title for a couple of words, and then the year. That's what I want, and you can change this any way you want. So that's what the name of the file is going to be when it's brought in, so you know what source is what. Now I don't want all of these in my main folder, so I'm going to add a folder called Sources, and I've got a slash there, so Sources is the folder, CiteKey is the file name. I'm going to do the same thing for the images. So I've got the Sources folder, and then the Images folder, then a folder for the citation key, and the image will then get a file name for however many images there are. But I also want to make a project folder, so I'm going to create a new folder called Projects, and I can drag the essay file into the Projects folder. So if I open it, put the essay file in the Projects folder, and let's just create the Sources folder. So I've now manually made the Sources folder. Let's just drag the source in there for the moment so you can see we've got the Sources folder and the Projects folder, and now I want to make a Templates folder. And if I right click and New Note, this is the template that Obsidian is going to look at to bring all of those highlights in from Zotero. I have this linked in the description below, but you can customize this in any way you want with all of this gobbledygook code if you want to go into it. But if you do want to customize it, you can, and I'm more than happy to help you out with that. So here we've got the year, and it's going to bring in the date of the source. Authors, and just bring in a list of all the authors. The title, the URL to the actual published page, so where you got it from. Then the PDF link, so this is going to link back to Zotero, which if you were to copy and paste into Word or Google Docs, you wouldn't get that. And then all of this is basically a loop that says, go to Zotero, find the highlight annotation, and then bring it in. And then do that again and again and again until you've got them all. And I'm also bringing in the comments and the tags of any annotations separately. So if we go back to Zotero and we have a look in here, we've got the annotation, that's the actual text itself. And then there's an option to add a comment and add a tag. In this one, you see we've got a comment, which I can change. So commented text, and then I've got a tag underneath it as well, and you can add more tags if you want. And when we come back to Obsidian, and I'm going to go to the settings, Zotero integration, then into the template file, we put Zotero template. So now it's got a template inside the settings. So now when we go to the command palette, Danny import, find the Zotero search, wherever it is, it may be hidden. Search for the Zotero items, so enter, now I want to enter this in, and it's going to fetch, find it, and you can see it's automatically created an images folder, and inside it, we have the folder for the citation key, and inside that, there is our image. So there's the table that we highlighted, and if I go to the file, here is the source with everything and the image in it. You can see it's brought in the year, it's brought in the authors, the title, the URL, going back to UC Science Direct, the Zotero link, the highlights that we had, and if I click on this, you can see it takes me to the highlight in Zotero. I'll just do that again. So if I scroll down, and let's click on this one, it's the, I'll bow, whatever that is, if I click on that, it will take me to the verbal highlight that I had inside of Zotero. So if you were to copy and paste from Zotero to Word, you wouldn't be able to jump back and then gain more context on the highlights. This lets you do that, and you can see we've got the added comments, we've got the tags in there as well, there's the comment, there's another comment, so it brings all of it in to Obsidian. Now I'm going to go to settings, the appearance tab, scroll down, you can see quick font size adjustment. I'm going to turn that one on, so now when I hold control on my keyboard and scroll in my mouse wheel, it zooms in and zooms out. I do this just for quick access, but it makes life a little bit easier in my opinion. Now this is one source. If I go to Google Scholar, you can see this is the two sources that I just brought in. If I click on this one, and now I want to quickly add this to Zotero, I can use the Zotero connector. So if I click on this, you can see it's going to find it, it's going to add it to my library. I can pick a collection if I want, but I'm just going to save it to my library. And if you don't have the connector on your browser, you can type in Zotero, scroll down, and you'll find Zotero connectors, or type in Zotero connector. Then when you click it, it should give you an option to install it on the browser you're on. I'm using Edge. If you're on Chrome or Firefox or Safari, it should say install for that browser. But as you can see, this is an academic paper, and it's selected an academic paper. If this was a video, then this would actually show a video icon. So now when I go to the Zotero My Library, there it is. And if we have a look, you can see it is a journal article. It automatically detected it was a journal article. It's also downloaded the PDF automatically. And this one doesn't have a tag, and that's because I haven't added the tag. So what I can do is go over to the tag section, add tag, go into my emoji bar. For me, that's Windows and full stop. I think Mac is command shift space maybe, but I can add the tag. And now once it's been added, that one is actually going to show. And that's because down in my tag pane, you can see there's the tag from the paper. But if we go over to the hourglass, I can right click and assign a color. Now this one's already got a color. It's orange. If it was a word, it would show in orange, but it's emoji. So it doesn't have an orange version of the emoji, but I can now select a position and the position goes up to nine or then show inside of this main area. And in addition to its location, so if I was to add another tag, you can see one, two, three, four, five, six, seven. I'm pushing the keys on my keyboard and it's adding all of those different tags. You can see all the way up to seven. Then when I push it again, so one, two, four, five, six, seven, it's going to remove all of those except from number three, which is the hourglass. So if, for example, I say, you know what? I've read all of these. That was holding shift on my keyboard and clicking. I can push three to say I'm not waiting because I'm going to push two and say, actually, I'm done. So let's go in and just actually highlight something. So I have actually done something. Yep, look, there we go. Some really important highlighted stuff. And let's just grab some red ones in there as well. That's obviously really important because I know exactly what I'm doing. Then we jump back to Obsidian. I go command palette, Danny import, find the paper, so long-term Flynn effect, enter, enter, and you can see it's appeared inside of the folder. And there we have all of our really awful highlights, but they're there. You can see that one's a red highlight. That one's a yellow highlight. And you can separate all of these out in loads of different custom ways, but I just want it in here to start with. And now I want to write my essay. Well, I'm going to remove all of these words because I don't need those. And how I set this out is I make a sources heading. So this is a heading one with a hash and then I go hash and then script. Then I make a heading two. So hash, hash, space, list, hash, hash, space, points. Then if I go to the top right and click on the expand button, then gives me these four different options and I want the outline. So it's going to show all of those headings and I can navigate up and down the file. And where Obsidian gets really cool is you can link inside of Obsidian. So if I go to points and I go square bracket, square bracket, it brings up a list of all of the files in my Obsidian vault folder. So if I go Dutton, there's that Dutton paper. And if I go Tease, there's the Tease paper. And these are both linked inside of the file. Why is that important? Well, if I right click on the tab and pin it, now this essay tab is going to stay where it is. If I click on this, it opens up the file. And again, if I drag this over, I now have a split screen. So I can click on that source, there's the source and there's the other source. So I can go between all the different sources and bring in the points I think are relevant. So let's just create some space. This point is important. So Control C, Control V. This point is important, Control C, Control V. And this image is actually really important. So I'm going to Control C and then drag that down, Control V. Now that was the Dutton paper. So if I copy that and then paste that link underneath this point, so I know where it comes from. This point, so I know where it comes from. And this table, so I know where it's come from. I can get rid of that link, Control D. And now I'm going to go to this next source. This point is actually related to this point. So I'm going to paste that underneath. And this point is actually related to this table. So I'm going to paste that underneath. Now I'm seeing a trend here. So I'm going to make a heading of Topic 1. And this is actually going to be another heading of Topic 2. So I'm going to copy that, paste it underneath that point, and paste it underneath that point. Remove the source at the top. So now I have the links going from the source to the highlighted point. And they go back to Zotero. If I now come to this source file and click on the backlinks panel, you can see it's linked to the essay. And it's showing I have two points that are linked there. I can expand it, and it shows me what's linked. If I go to the essay file and go to the outgoing links, you can see they are the two sources that I've linked, plus the image file. Now I'm writing my essay. Well, I want to start writing it. But I don't want to have to scroll up and down, because obviously that's just inconvenient. So what I can do is I can right click and then go split to write. So now I have the essay file open twice. I'm going to close down this tab. That was middle click with my mouse, so it's a scroll wheel. Now I can open up that outline again, go down to the script, and say introduction. Now in the introduction, I want to write about topic one. So I'm writing something really important. And that is this reference. So I can copy and then just paste it right in there. So I know, OK, this point was referenced here. Now what I tend to do is actually delete this, because I now don't need this point anymore. So I get rid of that. So my points list disappears, because I know I've processed it and started writing about it. You may want to keep them together. I personally don't. Now here you can see we've got two points that are the same or related in some way. I haven't actually read these, so they're probably not. But maybe I want to paraphrase both of these and say, this is good IQ stuff. That's the word IQ from there. And then different countries. That's just different countries from here. And I want to reference both of them. Well, I can just go copy, paste. And then in here, I go copy and paste. So now I've got the two different sources referencing one point. And now I don't need these anymore. So I can just delete all of those. Then I can cut it from here and then paste it underneath here. This is slowly starting to build out. But now let's just say I want to have a conclusion. Of course, I need to map out all the other sections as well. So we've got our literature review. We've got results. We've got a discussion. So we can jump backwards and forwards to any point of those documents. Let's go down to the conclusion. So this table has some interesting points. Maybe you want to say something about that. So the Flynn effect was in lots of countries. So I copy there, paste there. So now I've got the source. I can copy, paste it into the results. So these are some results. Maybe it's part of your lit review. So let's just X and then paste. So it was control X to cut, control V to paste. Now I don't need it inside of here. So I can get rid of that, get rid of those. And for the conclusion, actually, you know what? I like this, but I'm not entirely sure what this was talking about. So I'm going to click on the page one. Take me, okay, that's what it was talking about. I remember now it was something to do with this thing. I don't know. I'm making this up. So I come back. Then I can say whatever it is that I want to say about this thing. In the conclusion, we are getting dumber because that's what the reverse Flynn effect is about. Basically, you know what? I'm going to leave this there because I might add this into the discussion, but I'm not sure. So I'm just going to leave that there just in case. Now I have my essay written out in Obsidian with links back to the appropriate sources. As I write and as I think, maybe I go, oh, actually, you know what? If I go into this file, so you can see I've opened the source file straight away. I can see, oh, this was tagged with something or, oh, yeah, I had this idea. I may want to add that to the script. Well, I've got the essay file open over here so I can add it to the results. But maybe it was actually appropriate in the discussion. So this comment here that I made, actually, this came up with this idea in the discussion point. So I'm going to get rid of that one. Again, middle click on the mouse. You can see it's inside of the discussion section. So you can write and think at the same time going backwards and forwards between different pages. Again, you can have tabs. You can have multiple splits. So you can have it top, down the bottom. You can show or hide anything. And it just makes the writing and thinking space much cleaner for me. However, if you want to turn it into the university, well, that's where you're going to have to take it out of Markdown, out of Obsidian and into Microsoft Word. So I'm going to go settings, community plugins, browse. I'm going to go with Pandoc, install, enable, options. And you'll want to make sure you've got Pandoc installed on your device. So type Pandoc into whatever browser you use. Download the latest version. So go to the download page and then download it. I'm on Windows, so I'll download one of these. And then if you're on Mac, you'd download that. Linux, et cetera, et cetera. But once that's all downloaded, you can see you can change the internal links. So that's these things. At the moment, they've got two brackets on. You can change those so it turns into text. And if I open up that left sidebar, you see we're in the folder. This one is the essay file. If I close this down, this is the essay file. If I go to that command palette button again, search for Pandoc. I've just typed in Pan for short. And then Word. I'm now going to use the Pandoc plugin to export as a Word document. And you see exporting and successfully exported. So it is now inside of these folders, but we can't see it. Go down to settings, files and links. Now I want to detect all file extensions because it's been changed to a docx file. And there it is. So when I click it, I already have a saved Word document that was on my other screen here. So it's brought in the headers, it's brought in the links, and I've still got the link back to Zotero if I want it. But there is the script. This is where if you want this to be automatically cited properly, then you can use Pandoc information with bibliography files and CSL files. Or if you've already got it linked with Zotero, you've got your Word linked with Zotero, you can say, OK, I need to add a citation. This is the Dutton citation. So add. I'm going to use Harvard Elsevier. OK, let's just type in Dutton, the negative Flynn effect. That's the one. Let's go enter. And now it's been added in so I can get rid of that. Come down to the bottom and then go edit and add bibliography. Now I've added the Dutton bibliography. If I was to then copy that and then let's paste it in there because that's there as well. But we also need this citation. So I come onto there. Let's say add or edit because I copied the Dutton. We've got the Dutton 16. Let's go with, what's that, Ts? Yeah, there we go. So enter. Now I've got the two different citations. I push enter and it's got bigger because it's now added the two different citations in. So we can get rid of that bit from Word. But now the bibliography has extended. So we've got the Ts at the top of the other file. So Zotero and Word working together. This is how I would do it to make sure nothing is missed. If you were to do it automatically, of course, something could get missed. So I would copy and then backspace paste just to make sure that all the citations are in appropriately in the formatting that you want. But the main point here for me is with Obsidian, you can have the same file open twice. So the essay open twice. Or you can have sources open, go through sources. You can essentially puzzle, make all of the different points into the script with whatever outline you have or whatever running theory, concept, idea, philosophy value that you're working with. You can see all of the words at the same time. And it doesn't have to be one big long document on Word that you're scrolling up and down or you're clicking outline to navigate through. This for me works. Obviously, everyone is a little different.

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