How I research and write in Obsidian
Summary
TLDRThis 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
- ๐ Zotero helps collect, organize and cite research sources
- ๐ Obsidian provides a linked writing and thinking workspace
- ๐ก Zotero connector browser add-on simplifies capturing sources
- ๐ Obsidian links notes to their sources for context
- ๐ฅ๏ธ Use split view to see sources and notes side-by-side
- ๐ Write notes under topic headings in Obsidian outline
- ๐ Link related notes by topic for easy reorganization
- โ๏ธ Trim note excerpts once integrated into script
- โ๏ธ Pandoc exports Obsidian drafts to Word format
- ๐ 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
๐ 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.
๐ 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.
๐ 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.
๐ 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.
๐ 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.
Mindmap
Keywords
๐กreference manager
๐กnote taking
๐กobsidian
๐กlinking
๐กsplit screen
๐กoutline
๐กexporting
๐กautomated citing
๐กthinking and writing
๐กworkflow
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
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