YT YouTube2Text

YouTube2Text → Transcripts → 📜️ Zotero Research Paper Workflow | Full Comprehensive Setup Guide 🛠️

📜️ Zotero Research Paper Workflow | Full Comprehensive Setup Guide 🛠️ — Transcript

by Bryan Jenks · 8,968 words · 1,223 segments · language en · Watch on YouTube

Open in transcriber Summarize with AI Download SRT/VTT

Full transcript

0:00all right all right I know what you're
0:01thinking Brian why another zoto video
0:05well because it has come to my attention
0:07that people are still finding it too
0:09complex I reviewed some of my prior
0:11videos and I'm like yeah I guess if you
0:14don't live breathe this and you're
0:16constantly fiddling with things that
0:18yeah I guess it could be hard to follow
0:20so this is my uh newest attempt to do a
0:24comprehensive even down to install this
0:26application uh process of how to get
0:29complete set up to using my exact
0:32workflow and I'm going to be doing it in
0:34a sandbox Vault so we can see from
0:37beginning to end that everything works
0:39and functions in isolation not just in
0:42my Vault so there's nothing hidden
0:43nothing that I forgot about that's not
0:46connected like you're going to see
0:47everything connected the way that it's
0:49supposed to work end to end all the
0:51configuration everything and if you want
0:54the easy way to just copy paste and set
0:57this all up then my template vault is
0:59the way to go and I'll play a clip of
1:02that now want to get the latest releases
1:04of my obsidian template Vault and all of
1:05the work that I do in obsidian including
1:07the latest updates to my custom theme
1:09and CSS supporting me on GitHub sponsors
1:11at any recurring tier for any of those
1:12amounts we'll get you private access to
1:14the GitHub repository where all of my
1:16updates everything from my template
1:18vault is updated in near Real Time with
1:19constant updates tag releases and
1:21helpful documentation tutorials and
1:23other content specifically for sponsors
1:24only want to report issues that you find
1:26and have them resolv swiftly or just
1:27talk and have discussions about what you
1:28may have found or what you might have
1:29questions about in the template Vault
1:31and get prior prioritized responses from
1:32me and becoming a sponsor of my template
1:34repository will get you all of this and
1:35more thank you for your support I really
1:37appreciate it so as always my ultimate
1:38goal is to make everything as simple as
1:41possible so that I can help all of you
1:44be as successful as possible in setting
1:47up your personal Knowledge Management
1:49System your obsidian Vault what have you
1:51so let's get started and start with the
1:54absolute Basics so of course to get
1:56started you're going to need to download
1:58obsidian and I'll provide link links to
2:00all of these things in the description
2:02uh pin comment Y yada so we're going to
2:05download obsidian it's kind of obvious
2:07you need obsidian to use it then you're
2:09going to download
2:10zoto followed by the zoto better bib
2:15Tech plugin this is the only one that is
2:17required for the obsidian zoto
2:19integration plugin so we're going to
2:21download this you'll go to releases and
2:24again I'll just provide a link to this
2:25and the latest release is the one you
2:27want and what you're really after is
2:29this xpi file all we care about is this
2:33file so you can click this link and it
2:36will prompt you to download it and
2:38you're going to download it to a uh
2:41downloads area so tarot and you're going
2:44to download that particular plugin you
2:46can see I've actually already got an
2:48updated version there okay so once
2:50you've downloaded it what do you do well
2:53we're going to pop over into zoto zoto
2:56and you're going to go to tools add-ons
3:00and you can see I already have it
3:01installed here better bib tech for zota
3:04but in case you didn't all you have to
3:07do is go to that downloads folder find
3:11the xpi file drag it drop it and it will
3:15install install now and then restart
3:19zoto so now zoto is completely
3:22configured for what we need to do that's
3:24that's really it so we need to configure
3:26better bib Tech and we've installed
3:28obsidian so now we're going to start
3:30configuring obsidian for this part of
3:32the workflow we're setting everything up
3:34before we start doing the workflow we
3:36got to lay the structure in the
3:37foundation before we start building the
3:39house on top of it so now that zoto has
3:42the plugin installed we've restarted it
3:44it's good to go there's no P we're going
3:46to assume there's no papers there's no
3:48configuration there's nothing else
3:50you've done with zoto besides install it
3:52and add the plugin so now we're going to
3:54go and configure obsidian so there are
3:56several plugins that we're going to set
3:57up in obsidian so that you are having
3:59the workflow look and act and behave
4:02exactly like mine you might remove some
4:04of these you might change some of the
4:05settings some of the configuration
4:07perfectly fine but I'm going to show you
4:09how to set up exactly what I have the
4:12way that I have it so that it works
4:14exactly the way that you're seeing it
4:16work for me as I show it and demo it to
4:18you so you can follow along copy do
4:21everything I'm doing and you will have a
4:23setup exactly like mine at this current
4:26point in time so the first thing we're
4:28going to start off with an obsidian this
4:29is a blank Vault there's nothing in here
4:32absolutely no configurations there's no
4:35plugins uh if I open up the plug-in menu
4:38you can see there's no Community plugins
4:40installed there is literally nothing
4:42going on in here so Blank Slate we're
4:45going to create three folders I'm going
4:47to say I want an inbox folder I want a
4:51media folder I want it to not be spelled
4:56weird media and we want a templates
4:59folder
5:00okay so we got those three folders added
5:03good now we're going to actually
5:05download and install uh download and
5:09configure several obsidian plugins I'm
5:12going to give you a list of the plugins
5:13to install go ahead and install them and
5:15then we'll configure them so here we go
5:16this is the list of everything I want
5:18you to install and everything we're
5:19going to configure to do this full
5:21workflow in a comprehensive manner some
5:24of this stuff you could remove later on
5:25you can configure it to yourself in your
5:27own liking but install and activate all
5:30of these items so we see that there's
5:32one core plugin that's canvas everything
5:35else is going to be a community plugin
5:37so to get there you can do the hotkey
5:39control or command comma or this gear in
5:41the bottom left hand corner to settings
5:44Community plugins and make sure you turn
5:46on community plugins so once you have
5:48this you're ready to actually add them
5:50we're going to browse and we're going to
5:52actually install all of those plugins so
5:55we can already see like okay here's data
5:57view install that
6:01all right and now we're going to add um
6:05templat add
6:08that style settings I didn't list this
6:10one earlier but you you will need this
6:13for supercharge links so yes also
6:15install style
6:17settings okay and okay everything else
6:20is kind of hidden there okay so now
6:22we're going to install
6:27highlighter okay install highlight
6:30then we're going to
6:31do call out
6:37manager and then
6:40zero
6:46integration okay uh supercharged
6:54links we're going to add DB
6:58folder
7:03and I believe that's it for that so then
7:06we're going to go to core plugins and
7:07you're going to see that canvas by
7:09default is activated that's what we want
7:11so now we are ready to start configuring
7:14and just in case I'm going to make sure
7:16I update this style settings so these
7:20are the plugins that you need install
7:22them and now we are ready to configure
7:24them all right so now we're going to
7:26configure each individual plug-in now
7:29you can obviously just grab all these
7:31settings from my template Vault whether
7:32that's the sponsored live version or the
7:35static snapshot version I give away from
7:36my newsletter either way you could just
7:38copy and paste these settings from the
7:40obsidian directory it's the I believe
7:42the data. Json file but you can easily
7:45grab the settings from there or you can
7:48see the timestamp sections for this
7:49video and I'm going to do each
7:51individual plugin by itself so if you
7:53don't want to see a lot of boring
7:54configuration and you want to skip more
7:55to just here's what it looks like after
7:57you set that up and copy the settings
7:59later totally valid do that but now I'm
8:01going to get into each individual plugin
8:03for those that want to see the
8:04configuration for each individual plugin
8:07and how it works for the greater hole so
8:10let's start with templ all right so
8:12starting with templat we have a folder
8:15called templates and there's nothing in
8:17here at the moment now what I am going
8:18to do is I'm going to create a note I'm
8:19going to call it paper because we're
8:21going to paste the template there later
8:23but as for the plugin I'm going to open
8:25up the settings Community plugins we're
8:28going to go to templat
8:29we're going to turn it on and we're
8:31going to edit the settings by clicking
8:33the Cog so now what are we doing we're
8:35going to set the folder location where
8:37are my templates they are in the
8:38templates folder I'm going to turn on
8:41all of these settings except the last
8:44one because I don't care about that I'm
8:47going to turn off folder templates and
8:50everything else is default so these four
8:52options activated turn that one off I
8:54don't care about the folder templates so
8:57it's really just set the folder where
8:58are my templates and then these four
9:00options everything else is off and
9:02doesn't matter all right now we're going
9:03to begin with data view so Community
9:06plugins activate data view click the
9:08gear go to settings now just to
9:11replicate exactly my settings turn all
9:13of these on we are going to change this
9:17to 250 change that to ISO 8601 year
9:21month day I'm going to go here and do
9:23that hour hour minute minute least I
9:26believe that's hour hour minute minute
9:29okay and everything else can stay
9:31exactly the same that's it for data view
9:34so next we're going to configure the
9:35highlighter plugin this is going to
9:37affect the colors of your highlights as
9:39they come from zoto into obsidian when
9:41you export your note now for this to
9:44work effectively we're going to have to
9:45else also edit some CSS so we need to
9:48actually set up a theme so appearance
9:50and I'm going to say manage and I want
9:53the of course uh Grove box theme I'm
9:56going to do insanium Grove box install
9:59and use awesome okay so now we have that
10:03grub boox theme installed and we will
10:05then have a CSS file uh set up in you
10:08know the metadata folder which is going
10:11to be if I open up vs code file open and
10:16if I go to our new Vault let's
10:20do um desktop zoto Vault and we're going
10:25to do command shift period obsidian it
10:28should be theme
10:29obsidian Grove boox and theme. CSS this
10:33is what we want to open because there's
10:35going to be some CSS that we need to add
10:37for highlighter to work effectively so
10:39I'm going to go to my uh CSS theme grab
10:42my highlighter code copy it move it to
10:45the main theme paste it and inside of
10:49the theme the CSS file is we're using
10:52variables which these are the same color
10:54variables uh that are defined in the
10:56root of the custom theme which is a the
10:59obsidian grub Box by in insanium so this
11:02is saying hey the highlighter class for
11:04red has a background color of the
11:06variable bright red so if you define a
11:08variable bright red for any other theme
11:10or if the themes all use these standard
11:12variables these highlighter colors will
11:14change and adjust according to your
11:16theme dynamically and the important
11:18thing that I was having issues with is
11:19that using inline CSS or uh any of the
11:23other options with highlighter these
11:25important tags these important uh
11:27elements here were necessary to actually
11:29have the styling applied otherwise it
11:32just wasn't working for me whether it
11:34was reading view live view Source view
11:36doesn't matter so this is what I've
11:38gotten to work for me so I Define all
11:40these different colors and you can see
11:41the names red orange yellow Aqua Etc so
11:44if we go back to um well if we save it
11:47first save and if we go back to obsidian
11:51we're going to now go to the community
11:52plugins highlighter activate it click
11:55the gear for settings and then we're
11:57going to select CSS class es and I like
12:00realistic now the actual color codes
12:03here none of this matters at all unless
12:06you are going to do inline CSS but we
12:08don't care about that what we care about
12:10really is the names of these so red
12:13orange yellow these are the names we
12:15care about these correspond to our
12:17highlighter colors I'm not going to
12:19finish setting up all the colors I might
12:21I might be missing one or two or
12:23something but it doesn't matter actually
12:26you know what let's do it anyways so I'm
12:28going to say we don't want that one we
12:30got purple we need
12:32Aqua aqua and it doesn't matter what
12:36color we
12:37pick and let's add magenta and it
12:41doesn't matter what color we pick save
12:44save okay so now we have magenta and
12:47aqua and I believe that's the last of
12:48the ones we need red orange yellow aqua
12:51green is there yep okay blue purple
12:53magenta gray okay so everything should
12:55be represented so now because we have
12:58have our CSS classes overwriting and we
13:02have the names of the highlight colors
13:05added that the actual um hashtags don't
13:09matter for the colors because you'll see
13:10this in a second if I select this and
13:12you can saw you saw in our settings here
13:14we had this like Aqua was like a bluish
13:16color not green at all but if I select
13:19this text and I apply highlighter and I
13:23apply uh Aqua right here highlighter
13:25Aqua then highlighter Das aqua the class
13:30now it's green unlike the color in the
13:32settings which doesn't matter but inside
13:36of the CSS theme the highlighter Aqua
13:40this color is actually that green so
13:43this is why it's important the names
13:44need to be represented in the
13:46highlighter configuration just the names
13:48of these classes and doesn't matter if
13:50they're upper or lower case they all
13:51default to lower case when they're
13:52applied this then corresponds to the CSS
13:55code that applies the actual color and
13:58this is going to be what actually
14:00changes the highlight colors when you
14:02import your notes from zoto via the zoto
14:06integration plugin so this is one of
14:08those little finicky weird things but
14:10once it's set up okay you're good now so
14:12that's the highlighter plugin so now
14:14we're going to edit the call out manager
14:16this is going to be stylized blocks that
14:18I keep collapsed just to hold lots of
14:20metadata on a particular paper in an
14:22organized format that I can style
14:25customly customized customizable
14:27whatever so so call out manager this
14:30isn't one of those essential things you
14:31can always change and update this but I
14:33have a bunch of custom call outs and how
14:36they look uh is different based on some
14:39configuration changes I've made and it's
14:41actually a fairly large amount but if we
14:43go to the plug-in turn it on and edit
14:46the settings you can totally manage your
14:48call outs in here and rebuild all the
14:50custom ones that you want um you can see
14:53there's a bunch of default ones in here
14:54these are default from the plugin but
14:56for the ones that I like and I set up
14:59inside of uh your um so if I actually
15:04open up the configuration file for that
15:07call out so call out manager inside of
15:09our brand new Sandbox there will be a
15:11data. Json file produced by the plugin
15:16when you first activate it and it's
15:18pretty empty if I open the correct uh
15:22file there so our sandbox Vault obsidian
15:26plugins call out manager data Jon on and
15:29you'll see there's not a lot here now
15:31this is the one from my actual Vault not
15:35the um the sandbox we're working in so
15:37there's a bunch of custom ones that I
15:38have here and all this stuff is defined
15:41here so I'm just going to copy all of
15:45that because that is far easier than to
15:50do all of this from scratch so I'm going
15:53to delete all that and paste all the
15:55settings so again you can grab a copy of
15:58this from my template Vault either
16:01either place newsletter or the sponsor
16:03one so now with all those settings if I
16:05go back to our sandbox go to call out
16:08manager manage call outs there will be a
16:10bunch of new ones uh in here I might
16:13need to actually restart uh or reload
16:15the plug-in Force reload The Vault Force
16:18reload go back and then we're going to
16:21go to call out manager manage call outs
16:24and there we go I can see todoist
16:26authors methodology yeah a bunch of
16:29stuff in here that is now the stuff from
16:31my academic uh paper call outs okay so
16:35now we've configured call out manager
16:37it's really just setting up which what's
16:39the name that we target what's the color
16:41what's the icon because then we can
16:43actually do call outs where we say you
16:45know um author and
16:49um there we go and so then it might do
16:52authors and so then this is now targeted
16:55by that call out manager with custom
16:57theming so it's red it's got a
16:59particular icon and then we can do
17:01things like keep these things collapsed
17:03by default so you have to open them
17:05manually if you want to look at that or
17:07you can always automatically keep them
17:09expanded which defaults to open but if
17:12you're trying to hide a lot of
17:13information like I might like say 200
17:15related papers and it's just a list of
17:17data view related tags which is what
17:20happens sometimes I like to keep it
17:22collapsed with a minus so that way I can
17:24look at it if I want to but it doesn't
17:25make my paper just go like that when
17:28import something so this is what call
17:30out manager is doing and this is
17:31something I just started making uh
17:33prolific use of in my paper template and
17:36certain other templates where I want to
17:38really kind of condense a lot of
17:39information but still have it available
17:41okay now the most important one the
17:44meaty one which is the obsidian zoto
17:47integration plugin now there is one
17:49thing uh we need to do beforehand which
17:52is actually get my paper template into
17:55this Vault so I'm going to grab that
17:57from my actual Vault over here move to
18:00Source view okay grab all the content
18:03copy okay paper and I'm going to make
18:06sure I'm in Source mode and I'm going to
18:09paste all of this content all of this
18:12content so there's a bunch of stuff here
18:14a lot of stuff going on and we're going
18:16to see what this does later okay so now
18:18we're actually going to configure the
18:21plugin okay configuring the plugin and
18:24looking at the settings so Community
18:26plugins so tarot integration turn that
18:28on go to settings first thing is that
18:31you will need to have the PDF utility
18:33set up and installed just click the
18:35download button it will install it and
18:37add it to your Vault you're done once it
18:39says that nice so then what is the
18:43database it's going to be zoto and then
18:45where is the note import location we are
18:48going to change this to the inbox folder
18:51which we now we already have added
18:53that's the first thing we did we're
18:54going to open the created or updated
18:56notes after import that's what I have
18:58have we're going to enable annotation
19:02concatenation okay so then we're going
19:05to actually update the citation formats
19:08so I'm going to add a citation format
19:09and we're going to call this full
19:13citation and it's going to be a
19:16template and the template is not going
19:19to be anything yet this is um actually
19:22not something I'm using but this is what
19:24I currently have uh so that's fine I
19:28because this is I haven't done a full
19:29citation um this is going to be if you
19:31want the full actual like APA whatever
19:33FMLA FMLA FMA or what whatever the
19:37formatting styles are this would be
19:39where you configure that and you can do
19:40it with a template or latte bib Tech Etc
19:43but I haven't actually finished mine
19:44there so but I am going to add a second
19:46one which is the one I actually do use
19:48sometimes which is site it's going to be
19:50a template and it's going to be the um
19:54site
19:56key okay if I use that
19:59but the most important one is when we
20:00actually import the paper from zoto we
20:03need to have an import format this is
20:04what I was thinking of why I got
20:05confused so import format we're going to
20:08call this uh import paper and we're
20:12going to change the default output path
20:14to in inbox slite key. MD the image
20:19output path is going to be media SL zoto
20:24because I like to keep all my media just
20:26as a pool but sometimes like the zoto
20:28stuff I want that kept separate in case
20:29I need to do something with it slash
20:31site key slash okay then the image base
20:35name is going to
20:37be site
20:40key because I want the image to always
20:43be prepended with the actual citation
20:45key of Where It's associated with so if
20:47I search for that that something I can
20:49easily find images related to that
20:51particular paper citation key it's just
20:54handy so then the template paper we're
20:57going to type uh paper because it's in
21:00templates where our templates are
21:02actually located okay and scrolling down
21:05I prefer to use PNG they're nicer
21:08quality those are all defaults if you
21:10have Tesseract installed you can do OCR
21:13like you can just ignore this for all
21:15intents and purposes you can just ignore
21:16that um but I do have it set up but I've
21:19honestly never really like used it for
21:21anything so whatever but you can set
21:25that up as well and with that the um
21:28zoto integration plugin is correctly
21:30configured now so we could theoretically
21:33import papers we're going to do a few
21:34more voluntary um setups for the rest of
21:38the actual like workflow when we go end
21:40to end and work through the workflow but
21:41that is the setup for the zoto
21:44integration plugin in its entirety
21:47that's it okay now we're going to set up
21:49the more optional graphical changing
21:52nice quality of life polished stuff
21:55which we're going to start with
21:56supercharged links and style settings
21:58which I've done a couple videos recently
22:01about this so I'll put like links cards
22:04whatever you will see how to get there
22:06for that because that does a better
22:07explanation of all of that stuff but
22:10just to go over it all in one place
22:12we're going to activate supercharge
22:14links and style settings I'm going to go
22:16to supercharge links I'm going to set a
22:18new rule it's going to be a tag the tag
22:21is going to be um the inbox Emoji
22:24followed by the um the scroll Emoji
22:29followed by the Red Square Emoji I'm
22:31going to deselect all those so it's just
22:33that option save that okay I can leave
22:37all of those on I don't really think I
22:39need to change anything there let me
22:40double check supercharg
22:45links yep I leave all those on okay and
22:48then we go to style settings supercharg
22:50links the if the note has that tag
22:52what's the text I'm prepending it's
22:54going to be scroll Emoji space red
22:56square space and that's all we're going
22:59to do just for the sake of an example of
23:01supercharged links working that's it for
23:04those now if you want to have additional
23:07uh settings for that see my supercharged
23:09links uh video I cover all that in
23:11detail and you could also again grab my
23:15uh settings and configuration from the
23:16template Vault next we're going to
23:18configure DB folder because this is like
23:20the dashboard where I manage all of my
23:23uh inputs and most of my Vault it's
23:25really great for cutting through large
23:26swats of notes and easily organizing and
23:29cutting down to what you need to be
23:31looking at when you want to look at it
23:33so let us turn on DB folder go to the
23:36settings now I like Compact and going
23:40through the options here metadata I turn
23:43on these first three Skip One turn that
23:45one on okay enable inline Fields I turn
23:49that on I prefer top okay and scrolling
23:53through I turned both of these off all
23:57all right um I keep those times the way
24:00they are because they're ISO 8601 which
24:02is the best then uh leave all that the
24:06same file that's fine I turn that off
24:10turn that on auto update should probably
24:12turn on though but for the sake of
24:15example I have it off right now um and
24:17that's it for DB folder to configure the
24:20plugin that way now when we set up the
24:22workflow I will get to that point later
24:24when we actually implement the workflow
24:26with DB folder and the actual file I use
24:29but that's the settings for the plugin
24:31the configuration and lastly the core
24:33plugin canvas there's nothing to
24:34configure there it's just the the core
24:37plugin I don't think we really do any
24:39configuration on that uh oh wait there
24:42well I stand corrected there are options
24:43we can do with that did I change
24:46anything uh in the folder specifi below
24:48inbox pan show menu always all those on
24:52yep I changed nothing so the canvas
24:54plugin defaults exactly as that and with
24:56that everything everything is completely
24:59and correctly configured we are ready to
25:01actually import a zoto paper and do the
25:04full workflow so let's do that so let's
25:08work through the entire full workflow
25:10end to end you're going to add a paper
25:12to zoto now I'm assuming you've done
25:15this or you know how to do this uh you
25:17grab a DOI you can actually put the DOI
25:20here you can import it you can drag and
25:21drop at attach a file whatever so I'm
25:24assuming you know how to get a paper
25:26into zoto at this point
25:28so I'm just going to open something that
25:29I know will work for a fact which is I
25:32have a pdf version of unmasking autism
25:34by Devon price and if I open up this
25:37whole thing you it might take a bit but
25:41I have a bunch of highlights already in
25:42here now in my tag taxonomy note in my
25:45main vault which I can show over here
25:50tag tonomy if I drag that over here I
25:53can show you that so inside of this you
25:56can see I have different uh highlights
25:58mean different things for the papers and
26:00this is the strategy that I use these
26:02colors inside of the actual zoto notes
26:06so this is the scheme I use so inside
26:08zoto I actually do different highlight
26:10colors so we can see a bunch of red uh
26:13yellows over here but then there's a
26:14green uh there's an orange these
26:17correspond to the tag colors um or the
26:20the colors of the highlights that are
26:22going to be applied in obsidian so there
26:24are a few standard colors so yellow red
26:27green blue blue purple magenta orange
26:29gray these are all of the highlight
26:31colors that we use now I don't use all
26:33of these in my workflow but they're all
26:35set up to work with highlighter so that
26:38you can use all these colors and you can
26:39Define what they mean to you but
26:42everything else is already set up based
26:43on everything that you followed thus far
26:45in this video so now what I want to do
26:49is go to the beginning of this so we can
26:50see the example I'm going to
26:54do let's do alienation we're going to
26:57highlight that with a green and the note
27:00I'm going to add to that is alienation
27:04sucks all right so there we go we've
27:07added a new highlight I'm going to save
27:09it though I think it saves automatically
27:10we're now ready to actually import this
27:12into our vault we've imported a paper we
27:15highlighted something we took a note on
27:16that highlight and now we're going to
27:18actually import this uh research paper
27:21and all the highlights all the content
27:23everything into our obsidian vault as a
27:25file including even
27:28highlighted images and attachments so on
27:31page 30 here you can see I actually took
27:33like a screenshot highlight so this
27:35actually will capture the image and
27:36we'll see what happens with this when we
27:38import it so let's go ahead and import
27:40it so now it is worth mentioning that
27:41part of the speediness of my workflow is
27:43that I have a lot of uh hot Keys
27:45configured to do a lot of the different
27:47actions add a highlight insert templates
27:50open up the zoto thing I haven't
27:52configured any of that because I don't
27:53want you to be surprised if I'm just all
27:55on the keyboard doing stuff and it
27:56doesn't look right so you can set your
27:58key bindings to what you want them to do
28:01or you can grab my configuration from
28:03the template Vault I'm just going to be
28:04a dead horse just constantly reiterating
28:06that but you can also just open the
28:08command pallet and run the commands
28:10which is what I'm going to do for the
28:11sake of simplicity so we want to
28:13actually import the
28:15paper and how do we do that so we're
28:18going to run the command so I'm going to
28:19click open command pallet zoto and we're
28:21going to import paper now you can see
28:24there's a bunch of different items here
28:26these correspond to the import in
28:27templates citation templates everything
28:29that we've already configured in the
28:31plugins configuration now I want import
28:34paper because that's importing the
28:36entire paper and all its content using
28:38the template that we have copied from my
28:40prior Vault so it's going to say okay
28:43well what do you want from zoto I'm
28:45going to say unmasking and it should
28:46find it just fine price 2022 that sounds
28:49right enter now this might take a bit
28:52because there's a lot of content to sift
28:54through because it's a 300 plus page
28:56book and it's got to search through all
28:57all of that so I might make a cut and
28:59then bring it back to when it's done all
29:01right so it did finish importing it just
29:03took a while because it's a large file
29:05to scan but now it's finished and let's
29:08look at our results so if we open up
29:10media and inbox folders we can see
29:12there's some new stuff in here I didn't
29:13add anything this was all the actions of
29:15the plugin so okay there's some stuff
29:17here let's open up the file first so we
29:20can see that the name of the file is the
29:23name of the paper or in this case the
29:25book the date the current date today
29:28it's also has the symbol which is the
29:30Ampersand symbol which is this is all
29:32based off of my actual template uh the
29:35paper template because inside of this
29:36template you can see it says okay let
29:38title be title and then it actually adds
29:40the date and renames it with a symbol
29:43the date the title and I'll explain more
29:45about this uh in the workflow portion uh
29:48in a second but this is fairely
29:51important I can actually remove these
29:52things because we don't need those for
29:53supercharged links anymore but this is
29:56the p paper template you can see call
29:58outs there's stuff for data view there's
30:01data view key uh key value pairs there
30:03and there's all this um I believe it's
30:06called ginger templates and all this is
30:09here as well doing some stuff so inside
30:11of the output what we've exported it has
30:14a tag it has uh aliases of the site key
30:17and the actual title uh we don't need
30:19those for supercharge links anymore but
30:21now we have the call outs so here's the
30:23zoto link to the PDF the citation which
30:26is the site key we have the abstract we
30:29have keywords authors metadata it
30:33doesn't have those that's fine because
30:34it wasn't a paper it was a book related
30:36this is why I keep these collapses like
30:38look at all these related citations and
30:41it's by the citation keys because when
30:43you export that and it has related files
30:46from zoto you can say that it's related
30:48to the citation keys because inside of
30:50zoto if I go to here and I say related
30:54these are actually relating to all the
30:55papers the citations that I grabbed from
30:58the bibliography of the book I link them
31:00as related papers and so when you export
31:03this to to obsidian it actually grabs
31:06the citation keys of those related items
31:10in zoto so that now when I create new
31:13notes this is going to tie in to making
31:15sure that everything is linked so I can
31:17actually trace my citations and research
31:20even once it's inside of obsidian so
31:23I'll show you more about that in its
31:25specificity in a minute but continuing
31:27onwards there's nothing here that
31:29actually has a related uh link to this
31:32citation key because shocker uh I
31:35haven't imported anything else but we
31:37can actually see this work in our next
31:39example when I import something else so
31:41we'll see how this works in a bit
31:43hypothesis uh these are things that I
31:44would fill out manually as I do my
31:46review like what's my hypothesis about
31:48this paper the methodology results
31:50summary of key points whatever but
31:52here's the meat and potatoes that you
31:54probably care about here's the
31:55highlights here's a reference key for
31:57for what it what it means the colors but
31:59then hey here's that thing I did
32:01alienation alienation sucks and there we
32:03go this is actually the notes that I've
32:06taken inside of zoto and once I export
32:10it you can see there's a lot of yellow
32:11ah green okay there's the actual image
32:14there's the orange okay awesome because
32:17this grabs all the contents so we can
32:19see that this is an actual media file
32:21inside our media folder nice and inside
32:24of the actual text content here's the
32:26mark class highlighter orange so this is
32:28working with the highlighter plugin it
32:30has a link to zoto which if we go in
32:32there you can see it uses the zoto uis
32:35even though we don't have zot file
32:36anymore the plug-in zot file the old
32:38workflows you could see back on my
32:40channel in the past that would
32:42automatically build these links for you
32:43but now we can actually construct them
32:46manually via the template uh in my paper
32:50template because when we go here we can
32:53see open PDF library items The
32:55annotation attachment item key
32:57annotation page is the page and The
33:00annotation ID so when we actually build
33:02this dynamically we can recreate that
33:05functionality without needing the zot
33:07file plugin that is fantastic now I do
33:10have an issue here where some of these
33:13bullets are not connected correctly um
33:16that's likely just an issue of something
33:18I have going on in the template I might
33:20fix that later but what you can see is
33:23that everything is exported all the
33:24highlights all my notes on the
33:26highlights all of the links to the
33:28actual zoto item and even images so
33:32popping over um actually before we do
33:34that let's go all the way to the bottom
33:35is there anything else to look
33:37at
33:39uh okay so context significance these
33:42are just more things to manually fill
33:44out yourself based on the notes but that
33:47is everything that is all of the content
33:50that I've exported just from make adding
33:53a paper highlighting some stuff taking
33:55some notes there import it into obsidian
33:57and all of this is generated for you
33:59that's fantastic going to the media zoto
34:02folder we can see that it uses the site
34:04key as the name of the folder for the
34:06paper inside of there is all these
34:09different files that I've actually
34:10grabbed snapshots highlights or whatever
34:12of and it uses the site key prepended to
34:15name them so that way if I ever wanted
34:17to insert a particular image from uh the
34:21media folder into another file or
34:24whatever I can easily just search by the
34:26citation key and it gives me not only
34:28the folder but also all of the items and
34:31that makes it so much easier to just
34:33find exactly what I'm looking for
34:34because these are all of the images that
34:36I highlighted from that particular paper
34:38or book in this instance so now looking
34:41at the workflow the whole like inside my
34:44paper what's going on with this whole
34:46templator code I've actually had
34:47questions about this why do I have all
34:49of this here and this is very important
34:53is because when I import the paper into
34:56obsidian the default name of the paper
34:59is the citation key and I had issues
35:01before where I have these like data view
35:03queries here where I insert where
35:06contains related citation key now
35:10related I want to make sure I know
35:12everything else that is related to this
35:13paper so if I insert another paper and
35:15it has it's and it's related to
35:17unmasking autism I want it to make sure
35:20that that paper pops up in either query
35:23either way so I'm going to import
35:25another paper and show you what this
35:27looks like and how it might break or not
35:29work if we didn't have it set up this
35:30way so technically it wouldn't really
35:32break anything but I believe there were
35:34several issues I worked through that
35:36just made this make more sense so when
35:38you import the paper the default name of
35:41the object is the citation key nothing
35:44else but you know the way I like my
35:46papers and my inputs to be named is that
35:49it has like that special symbol and then
35:51it adds the date that I finished it and
35:53then the actual human readable name so I
35:55did not want the citation keys for that
35:56but I still wanted the papers to be
35:58findables by citation key that's why
36:00they have the aliases included so the
36:02Alias is the human readable name without
36:04even the date and the symbol as well as
36:06the actual citation key so both of those
36:08are added as aliases so I can find
36:10something but here's something actually
36:13interesting that you might not have
36:14thought of if I go into this particular
36:17note so unmasking autism's export for
36:20instance um I could say uh here is an
36:24interesting thing related to the paper
36:29add a link add a particular citation key
36:33so Lawson 2015a now this is a link to
36:36something that doesn't exist yet but I
36:38know that that's the citation key that I
36:39want to link to now I don't do this yet
36:43maybe I might you might but here's the
36:46here's the thing this paper doesn't
36:47exist yet because I haven't finished
36:48reading it I haven't imported it so if
36:50you take notes on things that are
36:52interrelated and reference them but you
36:54haven't created all the notes in your
36:56vault yet and you don't want to have to
36:58do all this extra stuff to just finish
37:00what what you're working on you can set
37:02this and forget it because now that I
37:06have this link to something that doesn't
37:07exist yet which is the citation key
37:09because I might not know when I finish
37:11that paper so the date might be
37:13different you can't plan ahead what the
37:15name of the note would be when you
37:17import it if you're following my
37:18workflow which uses the current day when
37:20you actually import the thing so because
37:23you can't plan that you're going to set
37:25the citation key because we know what
37:26the citation key is going to be so tarot
37:28has already set that it's exported
37:30things when you look at related it's all
37:32written here and so we could find
37:34related already once we go here Lawson
37:37200 2015a it's already listed and
37:40related but that's not a link like an
37:42obsidian link so if you're referencing
37:44this in links like this then this is
37:47where this whole part of the thing uh
37:49comes into play which is we first start
37:52off with the title of the paper is the
37:54citation key so then it says Ah yes the
37:56file exists we've created it it has the
37:59citation key this file exists now so
38:02after the file now exists the templator
38:04code will then run and say okay here's
38:07the title okay grab the date of today
38:10and then we rename the file with the
38:12Ampersand the date and the title so then
38:14because this has already connected this
38:16a link that didn't exist but does now
38:18based on citation key because obsidian
38:21updates all of the link references in
38:23the vault when you change the name of a
38:25file it Cascades and changes everything
38:27this will automatically update all of
38:29these broken links to the name of your
38:32file when you import it and forever more
38:35if you edit that file and rename it or
38:37whatever it will update all the links so
38:39let's see this in action I have the link
38:41it doesn't exist yet if I can hover see
38:43doesn't exist but now we're going to
38:45import it so if I run the command uh
38:48zoto import
38:50paper okay and I'm going to search
38:55for
38:57there we go okay A A striking there we
39:02go lawon at all 2015 enter it's going to
39:06then import that paper from zoto and all
39:08the metadata do you want to update
39:10internal links okay so always update
39:13because this is a Sandbox Vault I have
39:15this set so I never actually saw this
39:17come up so always update and so now we
39:19can see okay here's the name of the file
39:22here's the name of the link and you can
39:24see that it did in fact update because
39:26we change the name of the file when it
39:28was referenced now we can see that if I
39:30add a a pipe that there is the Alias to
39:34the site key but it's actually updated
39:36the name and that is very handy because
39:40now this exists but oh wait here we go
39:42where is this referenced because it
39:44contains related to Lawson so this is
39:46just using the data view stuff this is
39:48not an issue of actually linking back to
39:50it this is because of if I go to
39:53unmasking autism okay and we go to
39:55related
39:57up at the top was LW in 2015a because
40:00this paper this book is related to that
40:03paper inside of the paper we can see hey
40:06I'm related to this thing and this is
40:08all done Based on data view but when we
40:11actually have links to the name of the
40:13file and we use the citation key when we
40:15eventually import that file this
40:18particular workflow using my template
40:19will automatically update these links so
40:22that all the links now point to the
40:24correct thing so you do you can take
40:25notes reference a note uh or an exported
40:28paper using the citation key and then
40:30later on in the future when you actually
40:32import that because you finished
40:33processing it who knows when that might
40:35be we can actually see that uh there
40:38might be uh backlinks to where those
40:42notes are referenced and it's already
40:44there ready and waiting for you because
40:46if I import this paper today or a year
40:48from now I imported a masking autism a
40:51year ago or whatever it is and I
40:53referenced this note or this paper a
40:55striking reduction y yada and then I
40:58import it a year later because of that
41:00citation key link it updates and now it
41:03has a linked mention to the place where
41:06I made that link to the broken thing
41:08that didn't exist yet so this is why the
41:11workflow works that way and why the
41:13template is set up that way long
41:15roundabout example I probably just brain
41:17vomited all over the place but I hope
41:20that all that elaboration really makes
41:22that clear of why that works that way
41:25and the thought and reasoning behind
41:27that so now that we've gotten all these
41:30results like that's the pretty much the
41:31full workflow there's a few other extras
41:33I'm going to cover and that's going to
41:35be where supercharged links comes into
41:37play the DB folder plugin and uh the
41:40canvas workflow Now setting up database
41:42folder and showing the live example of
41:44that is going to be probably too much
41:46work that I want don't want to do in
41:47this video but again you can grab my
41:49configurations and yada yada but
41:52essentially all database folder is is a
41:55single data view query and I just say
41:57select everything from the Vault and
42:00then I add um filters and filter groups
42:04to this particular
42:07um uh View and that Progressive
42:10filtering is what Narrows down exactly
42:13what uh I want to see from that view so
42:16if I actually showed um my database
42:19folder plug-in uh view from my personal
42:21Vault you can see I have all these
42:23different tag groups here so when I look
42:26at them you can see okay it's just a
42:27bunch of different tag groups and and
42:30statements it's ultimately showing uh
42:34all of the different options for inputs
42:36and uh status so when I progressively
42:38filter and I say okay show me all the
42:40red podcast notes then once this stops
42:44lagging it would show you a filtered
42:46view of just all of the red podcast
42:48notes there we go so I forgot to click
42:53the filter thingy but now I can say okay
42:56show me all podcasts by clicking the
42:58podcast item and then it shows me all
43:00the different ones in different stages
43:01of processing only the incomplete ones
43:04there we go or I can just say show me
43:06the yellow ones and there we go single
43:08one so using database folder this simply
43:10lets me look at all of my input notes um
43:15because I have these filters that show
43:17those different options but also there's
43:18just the global filters of the tag needs
43:21to contain the inbox Emoji because that
43:23means that it is an input note uh so as
43:27long as it has that inbox Emoji which
43:29all of these do it's all contained in
43:31the nested tags they all get picked up
43:33then it's the progressive filtering of
43:35status and symbol and I'll do a whole
43:36video on database folder uh coming up
43:39soon to explain how I configured and
43:42fully set up the database folder but
43:43again you can always just grab the
43:44configuration from my template Vault but
43:46this is what I'm using to really manage
43:49all of the inputs across the Vault
43:50keeping it all in just one folder I
43:52don't have to file anything there's
43:54nothing weird there and then I can use
43:55this to to filter through and sift
43:57through everything and again the links
43:59use supercharged links so I can see all
44:02those symbols here as well so it's all
44:04really just in the title uh and that's
44:07really helpful to help manage it and
44:08then finally I did do a video about my
44:11canvis based workflow especially for my
44:13research on autism and so if I created a
44:17new canvas create new canvas what I have
44:20been doing is doing things like okay I
44:22have my uh research open on one side and
44:25then I have canvas open on the other and
44:27I might say okay I have a particular
44:30thing I'm talking about so let's just
44:31say um what I like what I want to talk
44:34about is uh alienation in
44:40autism and so that is something it
44:42doesn't exist yet it's not a note it's
44:43just a particular node in the canvas and
44:47so I can say that um there might be
44:49something um I want to relate to that
44:52particular item there and so what I can
44:54do is I can say say uh bang open a link
44:58unmasking autism and so I could do uh
45:02that followed by the
45:05um particular let's
45:08do that
45:11one um actually I don't want the Alias I
45:13wanted unmasking autism because I want
45:15to do a uh what is it a block
45:20transclusion so I know that um and
45:23here's here's the tip is that if you
45:24have a lot of exported notes from a
45:26paper and you're trying to grab the
45:27citations doing this workflow the way
45:29that I did it in my video on obsidian
45:31canvas links card whatever elsewhere
45:34you'll see it pop up one of the key
45:36tricks I was doing is that I just kept
45:38this particular portion of um the
45:42text uh copied so I would just do this
45:45right
45:45here okay and so if I'm just if I'm
45:48doing a bunch of work on this I'm going
45:49to say okay I'm going to go through
45:50these items and I want to actually list
45:52off things and do this so I would then
45:54paste that because it has all the name
45:56all the transclusion everything ready
45:58for me to then say what exact thing are
46:00you looking for so then if I have a ton
46:02of stuff like I do for this particular
46:03book what I've been doing is I do that
46:06whole you know paste that standard block
46:08and then I know that this is on page
46:09nine so I can say page Space 9 and then
46:14this filters it down very easily to what
46:17I might be looking for here so bam or I
46:20might even just say hey we're going to
46:22uh keep the whole thing set to page like
46:25that so so then I can just say paste and
46:27now it's ready for page searching page
46:30nine bam and so now I can actually
46:32import that if I click off of it so
46:35here's the whole citation it's added a
46:37block reference and now I have this
46:39included here and now I can include this
46:41note link it to that and that's
46:43basically what I've been doing in my
46:44research you can watch the whole link
46:46video as I do it but this way I can
46:48actually grab the notes and Link it to
46:51that particular thing now one thing to
46:54note as a note of caution is is that if
46:56you make changes in zoto and repport
46:58this note this is going to override all
47:00this stuff all your work all your
47:02content all the block references
47:03everything's going to be lost so the key
47:06part of my workflow is that I don't
47:08export multiple times if you need that
47:11then certain aspects of my workflow will
47:12need to be adjusted to suit your use
47:14case I particularly
47:17particularly prefer to do all the work
47:21export the content and then work with
47:23the content in obsidian primarily I I
47:25don't usually go back and do other stuff
47:27because remember I'm not an actual
47:30academic I like looking at academic
47:31resources and taking notes on it but I
47:33don't actually work in Academia so maybe
47:35this workflow is not ideal for actual
47:38academics but it's something to work
47:39with that you can then tweak and suit to
47:41your own needs and use cases but
47:45hopefully this overview of full setup
47:47really helps again you can grab a lot of
47:49these configuration settings all the
47:51stuff that I got in my template Vault
47:53whether that's from my live sponsored
47:55version that has The Cutting Edge stuff
47:56that I make even weeks advance of
47:59uploading videos talking about stuff
48:00people have instant support instant
48:03access or there's the static snapshot of
48:05My Vault that I do update update on
48:08various releases when I get my template
48:10Vault to a stage where it's ready to
48:11have a new release so hopefully that
48:14helped let me know your thoughts
48:15comments issues questions anything in
48:18the comments I'd love to hear from you
48:19and I will catch you all in the next
48:24one
48:27[Music]

About this transcript

This page contains the full transcript of 📜️ Zotero Research Paper Workflow | Full Comprehensive Setup Guide 🛠️ by Bryan Jenks, generated from the public captions YouTube serves with the video. The transcript has 8,968 words across 1,223 segments, with the original timestamps preserved so you can click any line to jump to that moment in the embedded player.

What you can do with it

Use the transcript to take notes, quote the speaker, build a study guide, generate a summary with ChatGPT or Claude via the YouTube Summary tool, or export it as a timed subtitle file with YouTube to SRT. You can also re-open it in the transcriber to translate the transcript into 100+ languages.

Free YouTube transcript tool

YouTube2Text is a free YouTube transcript generator — no signup, no daily limit. Paste any YouTube link and get the full transcript instantly, with timestamps, click-to-jump, translation to 100+ languages, AI prompts for ChatGPT, Claude, and Gemini, and exports to TXT, SRT, VTT, or Markdown.