How I research and write in Obsidian

Summary

This video script delves into a detailed tutorial on how to effectively organize and write an essay using digital tools, emphasizing the process beyond the basic structure. It introduces Zotero as a reference manager and Obsidian for note-taking, highlighting their roles in managing sources, annotations, and links between ideas. The script explains how to integrate these tools, from importing highlights and notes from Zotero into Obsidian, to structuring thoughts and references in a coherent manner. It also covers the transition from markdown to a formatted Word document, ensuring a seamless workflow for academic writing. This guide provides invaluable insights for anyone looking to enhance their essay writing process with technology.

Takeaways

• 😀 Zotero helps collect, organize and cite research sources
• 📚 Obsidian provides a linked writing and thinking workspace
• 💡 Zotero connector browser add-on simplifies capturing sources
• 🔗 Obsidian links notes to their sources for context
• 🖥️ Use split view to see sources and notes side-by-side
• 📝 Write notes under topic headings in Obsidian outline
• 🔀 Link related notes by topic for easy reorganization
• ✂️ Trim note excerpts once integrated into script
• ⚙️ Pandoc exports Obsidian drafts to Word format
• 📄 Zotero and Word integrate to auto-generate bibliography

Q & A

What reference manager software is used in the video?

Zotero is used as the reference manager software.

How are highlights and notes from reference sources brought into the writing software?

A Zotero integration plugin for Obsidian fetches highlights and notes through a template, automatically creating backlinks to reference sources.

What writing software is demonstrated?

Obsidian is used as the writing software.

How does the writing setup in the video allow referencing sources while writing?

By using Obsidian's link feature, sources can be pinned open and linked directly in the text for easy access and referencing while writing.

Why are notes processed from reference manager to writing software rather than directly copying?

To maintain links back to sources and context for highlights that would be lost when directly copying.

How are multiple reference documents handled?

Obsidian's split screen allows multiple reference documents to be open simultaneously for easy cross-referencing.

How can the text be exported for use in other software?

The Pandoc plugin for Obsidian allows exporting the text to Word while retaining headings, links, and formatting.

How are citations handled when exporting to Word?

Zotero integration in Word helps ensure citations are properly formatted, and manual checking helps catch any missed citations.

What ensures highlights have contextual links back to sources?

The Zotero integration imports highlights as text snippets with links back to the location in the source PDF.

How are notes organized within the writing software?

Headings and an outline view in Obsidian allow textual notes to be structured logically.

Outlines

00:00

😀 How zotero is used to collect and organize sources and highlights

The paragraph explains how zotero is used to store, organize and highlight information from sources. It shows how to create a zotero library, add sources, highlight text, add tags and comments. It also mentions useful zotero plugins like Better BibTex.

05:01

😀 Setting up the Better BibTex plugin and customizing citation keys

The paragraph shows how to install the Better BibTex plugin to customize the citation key format in zotero to author name, short title and year. This citation key is used when importing highlights into Obsidian.

10:01

😀 Collecting highlights from sources and bringing them into Obsidian

The paragraph demonstrates using the zotero integration in Obsidian to import highlights from zotero sources. It shows setting up folder structure in Obsidian vault and the import template. On import, highlights are brought in with links back to source PDFs.

15:02

😀 Structuring and writing the essay in Obsidian

The paragraph explains how to structure the essay outline in Obsidian with headings and links to sources. It shows writing the essay by connecting points to sources. Unneeded points can be deleted when processed. Multiple file panes allow navigation.

20:02

😀 Exporting the Obsidian markdown essay into a Word document

The paragraph demonstrates using the Pandoc plugin to export the Obsidian markdown files into a Word document. It retains headings and links back to zotero. Citations can be added in Word using zotero integration.

Keywords

💡reference manager

A reference manager like Zotero is used to organize sources and references for research. In the video, Zotero is used to store sources, highlight information in the sources, and link back to these highlights from the essay.

💡note taking

The presenter shows how to take notes on sources in Zotero using highlights and comments. These notes and highlights can then be brought into the essay writing software Obsidian.

💡obsidian

Obsidian is a note taking and knowledge management software that allows linking between notes. The presenter uses it to write the essay, linking back to the Zotero notes.

💡linking

Obsidian enables linking between notes and sources. This allows easy cross-referencing while writing the essay in Obsidian.

💡split screen

Obsidian supports split screening, allowing the user to view multiple notes/documents side-by-side. This assists writing by enabling access to sources and outline.

💡outline

Obsidian can show an outline of the document, helping to navigate longer pieces of writing.

💡exporting

Once finished, the markdown Obsidian document can be exported to Word using Pandoc. This maintains much of the formatting and linking.

💡automated citing

Zotero integration allows automated citation in Word after exporting from Obsidian, ensuring citations are not missed.

💡thinking and writing

A key advantage highlighted is that Obsidian enables thinking (notetaking, linking) and writing in one space, rather than separate documents.

💡workflow

The video focuses on demonstrating an effective workflow for research and essay writing leveraging multiple pieces of software.

Highlights

Use Zotero as a reference manager to store sources and notes

Obsidian lets you visualize connections between sources and write simultaneously

The Zotero browser connector simplifies saving sources to your library

Better BibTex for Zotero improves citation key formatting

The Obsidian Zotero plugin imports highlights, comments and tags

Custom templates control how Zotero data is imported into Obsidian

Obsidian graph view visualizes connections between notes

Splitting notes helps navigate files while writing

Link notes to sources so you can verify context

Reorganize notes into outline structure while writing

Export Obsidian notes to Word while retaining links

Zotero and Word integrate for automated citations

Visually connect sources to writing helps avoid missing info

Non-linear writing workflow surfaces insights and connections

Frequent link checking provides context and consistency

Transcripts

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 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 rewrite and we

write and we 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 Tero 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

zoto alongside all of the other

information so dii 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 a highlight manager essentially

you can 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 zoto 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 high

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 is an 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

zota 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 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 I read

one article then I read another article

and it was just a long list of a loot of

points that I 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 ESS 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 screen 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 set settings now I personally prefer

this to be dark mode so I'm going to

change this to dark mode going to go to

community plugins turn on community

plugins

browse type

zoto install enable options I'm going to

download the PDF utility so it can read

the PDFs make sure it's the zoto

database scroll down I now want an

import format cuz I want to import

highlights and going to name it Danny

import now citation key is what the file

is going to be called if we go back to

zota 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 biex for zoto if you

search for better biex for zoto 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 5 days ago go for me once

it's downloaded it I can then drag it

into this window and then it restart

sotero so it will update itself and say

hey you've now got better bib Tex for

zoto so I've got my download here I then

drag it in and it gives me the popup

window obviously I've done it so I'm not

going to say install now cuz I've

already got it there now when I go to

edit I go to

preferences I go to the better bib deex

preferences and say open those

preferences I can then customize the

citation key formula and for me i' 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

anywh 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 site key

is the file name and 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 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 with 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

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 zoto I have this

Linked In the description below but you

can customize this in any way you want

with all of this go 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

publish page so where you got it from

then the PDF link so this is going to

link back to zoto which if you would 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

zoto 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 zoto 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 zoto integration

then into the template file we put

zotter template so now it's got a

template inside the settings so now when

we go to the Comm command pallet Danny

import find the zoto search wherever it

is it may be hidden search for the zoto

item 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 you can see

science direct the zoto link the

highlights that we had and if I click on

this you can see it takes me to the

Highlight in zoto I'll just do that

again so if I scroll down and let's

click on this one it's the AR Bal

whatever that is if I click on that it

will take me to the verbal highlight

that I had inside of zoto so if you were

to copy and paste from zota to word you

wouldn't be able to jump back and then

gain more context on the high 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 I hold control on my

keyboard and scroll in my mouse wheel it

zooms in and zooms out I do this just

for 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

zoto I can use the zoto connector so if

I click on this you 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 zoto scroll down and you'll find zoto

connectors or type in zotter connector

then when you click it it should give

you an option to install it on the

browser your own on I'm using Edge uh 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 zoto 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 uh 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 color now

this one's already got a color it's

orange if it was a word it it would show

in Orange but it's an 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 9 will then

show inside of this main area and in

addition to its location so if I was to

add another tag you can see 1 2 3 4 5 6

7 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 1 2 4 5 6 7

is 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 it

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 well

that's obviously really important

because I know exactly what I'm doing

then we jump back to obsidian I go

command

pallet Danny import find the paper so

long-term Flyn 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

space

list hash

space

points then if I go to the top right and

click on the expand button then gives me

the 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 dton

there's that datton paper and if I go

te's there's the te's paper and these

are both Linked In ins side 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 contrl Ctrl V uh this point

is important crl c contrl v and uh this

image is actually really important so

I'm going to crl C and then drag that

down crl 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 uh 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 one and this is

actually going to be another heading of

topic two so I'm going to copy that

paste 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 zoto if I now come

to this source file and click on the

back Links 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

to have to scroll up and down because

obviously that's just inconvenient so

what I can do is I can rightclick and

then go split to right so now I have the

essay file open twice and going to close

down this tab that was middle click with

my mouse so it's a scroll will now I can

open up the 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 okay 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 there

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

uh 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 got a 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 Flint 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 result so these are some

results maybe it's part of your lit

review so let's just X and then paste so

those crl X to cut contrl 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 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 flim effect is about

basically you know what I want to leave

this there cuz 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 in 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 sa file open

over here so I can add it to the results

but maybe it was actually appropriate in

the discussion so this 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 and 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 going to go

settings Community plugins and browse

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 download that Linux

ET etc etc 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 text and if I open up that left

side barar 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 pallet 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 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 you still I've still got

the link back to Zer 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 zoto you've got your word

linked with zoto you can say okay I need

to add a citation this is the Dutton

citation so add I'm going to use Harvard

elevia okay let's just type in dton the

negative Flint 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 duton

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 on to there

let's say add or edit cuz I copied the

dton we've got the dton 16 let's go with

what's that te's 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 tside at the top of the other file

so zoto 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