How I research and write in Obsidian

Danny Talks Tech
16 Feb 202422:43

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

  • ๐Ÿ˜€ Zotero helps collect, organize and cite research sources
  • ๐Ÿ“š Obsidian provides a linked writing and thinking workspace
  • ๐Ÿ’ก Zotero connector browser add-on simplifies capturing sources
  • ๐Ÿ”— Obsidian links notes to their sources for context
  • ๐Ÿ–ฅ๏ธ Use split view to see sources and notes side-by-side
  • ๐Ÿ“ Write notes under topic headings in Obsidian outline
  • ๐Ÿ”€ Link related notes by topic for easy reorganization
  • โœ‚๏ธ Trim note excerpts once integrated into script
  • โš™๏ธ Pandoc exports Obsidian drafts to Word format
  • ๐Ÿ“„ 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

๐Ÿ˜€ 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

๐Ÿ˜€ 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

๐Ÿ˜€ 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

๐Ÿ˜€ 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

๐Ÿ˜€ 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

๐Ÿ’กreference 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.

๐Ÿ’กnote 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.

๐Ÿ’กobsidian

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.

๐Ÿ’กlinking

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

๐Ÿ’กsplit 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.

๐Ÿ’กoutline

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

๐Ÿ’กexporting

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

๐Ÿ’กautomated citing

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

๐Ÿ’กthinking and writing

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

๐Ÿ’กworkflow

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

play00:00

most how to write an essay videos that

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I've seen talk about the structure and

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the outline so introduction research

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discussion conclusion all those sorts of

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things but I don't see how they actually

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do it with the the technology yes they

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use word and maybe a reference manager

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but what is it that they're doing to get

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the highlighted points into the script

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because we think and rewrite and we

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write and we we think we sort of do it

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at the same time and I've always been

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lost as to how other people have done it

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so this is how I do it I use Tero as a

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reference manager so it's basically a

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library of all of the sources and you

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can see here I've got two sources at the

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top that I've added I've got a citation

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key which is like an ID for each of them

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and it's done automatically inside of

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zoto alongside all of the other

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information so dii URL authors title Etc

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and when I double click it opens up a

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tab and you can see I've already got

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some notes in here and I can highlight

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so I've got the pen up here so I can

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highlight whatever words I want if I

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change the color to let's say green I

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can then highlight in a different color

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they all appear in the sidebar which I

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can navigate to quickly and easily so

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that's a a highlight manager essentially

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you can see I've got a Post-It note

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there I could just add a Post-It note

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anywhere I want and add notes so let's

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say adding a comment so now I've got a

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comment on a green note in here you can

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see I've added a comment and a tag to

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the Highlight so I can tag the Highlight

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as well as add a comment to the

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highlight of my thoughts or ideas of

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whatever it is about this point and as I

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scroll down you can see I've got a table

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I can come into here and then drag

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around I don't want that to be green so

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let's just change that highlight to

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Yellow now I have a yellow highlight I

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can navigate between the green

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highlights the yellow highlights or the

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tag I can go between whatever I want

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inside of zoto but that's just getting

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the points as I come back I can then

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double click and open up another one so

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let's just say I've got some high

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highlighted points in here as well but

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how do I bring all of these points into

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a place to write I could go backwards

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and forwards between them which

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obviously is an ideal I could copy and

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paste them into a word doc which is what

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I've done previously but if I do a copy

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and paste how do I get from word the

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copy and pasted text from word back to

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zota well I'd need a link and I don't

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want to have to manually make a link

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coming backwards and forwards and I

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don't really want to come into here and

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then search for the file or the paper or

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whatever it is and then try and find the

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Highlight that that's just too much

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effort to be honest and when I'm working

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in word I used to have two different

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word documents up so I'd have a writing

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document and then a planning document

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and the planning document would have

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tons of all these different notes

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sporadically put around but I wouldn't

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have any order to them because I I read

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one article then I read another article

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and it was just a long list of a loot of

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points that I I couldn't like puzzle

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piece put together and for me Obsidian

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solves those issues so if I create a

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vault it's basically a folder on my

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computer I'm going to call it essay demo

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and then I'm going to browse and find

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the external hard drive let's select

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folder and then create so it's now

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created a folder called ESS demo on my

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computer and I have one file in it

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called Welcome this is Obsidian going to

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my external hard drive you can see essay

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demo if I double click in there's all of

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the setting files and there's the actual

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file the welcome. MD file now if I was

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working in word I would have to have two

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or three different word files up if I

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change the name of this to

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essay and then let's add a new note and

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call it Source you can see I've actually

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got two different files up at the same

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time split screen so I don't need to

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have to have two different word

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documents open and if I drag this in the

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middle now I've got three so I can have

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three documents open or I could have

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multiple tabs so multiple sources up on

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one side and then my essay over on the

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other side but before we get ahead of

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ourselves let's actually bring in those

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highlights so I'm going to go down to

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the set settings now I personally prefer

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this to be dark mode so I'm going to

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change this to dark mode going to go to

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community plugins turn on community

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plugins

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browse type

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zoto install enable options I'm going to

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download the PDF utility so it can read

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the PDFs make sure it's the zoto

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database scroll down I now want an

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import format cuz I want to import

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highlights and going to name it Danny

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import now citation key is what the file

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is going to be called if we go back to

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zota you can see we've got the two

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different items there and they both have

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unique citation keys I personally use

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and would recommend using an add-on

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called better biex for zoto if you

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search for better biex for zoto you'll

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find this page and then we go to the

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install latest release then we want to

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download the xpi that's the most recent

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one that was 5 days ago go for me once

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it's downloaded it I can then drag it

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into this window and then it restart

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sotero so it will update itself and say

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hey you've now got better bib Tex for

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zoto so I've got my download here I then

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drag it in and it gives me the popup

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

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going to say install now cuz I've

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already got it there now when I go to

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edit I go to

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preferences I go to the better bib deex

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preferences and say open those

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preferences I can then customize the

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citation key formula and for me i' put

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the author then the short title for a

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couple of words and then the year that's

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what I want and you can change this

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anywh you want so that's what the name

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of the file is going to be when it's

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brought in so you know what source is

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what now I don't want all of these in my

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main folder so I'm going to add a folder

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called sources and I've got a slash

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there so sources is the folder site key

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is the file name and I'm going to do the

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same thing for the images so I've got

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the sources folder and then the images

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folder then a folder folder for the

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citation key and the image will then get

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a file name for however many images

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there are but I also want to make a

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project folder so I'm going to create a

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new folder called projects and I can

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drag the essay file into the projects

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folder so if I open it with the essay

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file in the projects folder and let's

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just create the sources folder so I've

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now manually made the sources folder

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let's just drag The Source in there for

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the moment so you can see we've got

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sources folder and the projects folder

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and now I want to make a templates

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folder and if I right click and new note

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this is the template that obsidian is

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going to look at to bring all of those

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highlights in from zoto I have this

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Linked In the description below but you

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can customize this in any way you want

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with all of this go code if you want to

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go into it but if you do want to

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customize it you can and I'm more than

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happy to help you out with that so here

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we've got the year and it's going to

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bring in the date of the source authors

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and just bring in a list of all the

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authors the title the URL to the actual

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publish page so where you got it from

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then the PDF link so this is going to

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link back to zoto which if you would to

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copy and paste into word or Google Docs

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you wouldn't get that and then all of

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this is basically a loop that says go to

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zoto find the Highlight annotation and

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then bring it in and then do that again

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and again and again until you've got

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them all and I'm also bringing in the

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comments and the tags of any annotations

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separately so if we go back to zoto and

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we have a look in here we've got The

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annotation that's the actual text itself

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and then there's an option to add a

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comment and add a tag in this one you

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see we've got a comment which I can

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change so commented text and then I've

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got a tag underneath it as well and you

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can add more tags if you want and when

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we come back to obsidian and I'm going

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to go to the settings zoto integration

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then into the template file we put

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zotter template so now it's got a

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template inside the settings so now when

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we go to the Comm command pallet Danny

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import find the zoto search wherever it

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is it may be hidden search for the zoto

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item so enter now I want to enter this

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in and it's going to fetch find it and

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you can see it's automatically created

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an images folder and inside it we have

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the folder for the citation key and

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inside that there is our image so

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there's the table that we highlighted

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and if I go to the file here is the

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source with everything and the image in

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it you can see it's brought in the year

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it's brought in the authors the title

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the URL going back to you can see

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science direct the zoto link the

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highlights that we had and if I click on

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this you can see it takes me to the

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Highlight in zoto I'll just do that

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again so if I scroll down and let's

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click on this one it's the AR Bal

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whatever that is if I click on that it

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will take me to the verbal highlight

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that I had inside of zoto so if you were

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to copy and paste from zota to word you

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wouldn't be able to jump back and then

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gain more context on the high highlights

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this lets you do that and you can see

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we've got the added comments we've got

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the tags in there as well there's the

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comment there's another comment so it

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brings all of it in to obsidian now I'm

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going to go to settings the appearance

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tab scroll down you can see quick font

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size adjustment I'm going to turn that

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one on so now I hold control on my

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keyboard and scroll in my mouse wheel it

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zooms in and zooms out I do this just

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for for quick access but it makes life a

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little bit easier in my opinion now this

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is one source if I go to Google Scholar

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you can see this is the two sources that

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I just brought in if I click on this one

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and now I want to quickly add this to

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zoto I can use the zoto connector so if

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I click on this you see it's going to

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find it it's going to add it to my

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library I can pick a collection if I

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want but I'm just going to save it to my

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library and if you don't have the

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connector on your browser you can type

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in zoto scroll down and you'll find zoto

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connectors or type in zotter connector

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then when you click it it should give

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you an option to install it on the

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browser your own on I'm using Edge uh if

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you're on Chrome or Firefox or Safari it

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should say install for that browser but

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as you can see this is an academic paper

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and it's selected an academic paper if

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this was a video then this would

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actually show a video icon so now when I

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go to the zoto my library there it is

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and if we have a look you can see it is

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a journal article it automatically

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detected it was a journal article it's

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also downloaded the PDF automatically

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and this one doesn't have a tag and

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that's because I haven't added the tag

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so what I can do is go over to the tag

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section add tag go into my emoji bar for

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me that's windows and full stop I think

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Mac is command shift space maybe uh but

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I can add the tag and now once it's been

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added that one is actually going to show

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and that's because down in my tag pane

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you can see there's the tag from the

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paper but if we go over to The Hourglass

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I can right click and assign color now

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this one's already got a color it's

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orange if it was a word it it would show

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in Orange but it's an emoji so it

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doesn't have an orange version of the

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Emoji but I can now select a position

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and the position goes up to 9 will then

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show inside of this main area and in

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addition to its location so if I was to

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

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7 I'm pushing the keys on my keyboard

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and it's adding all of those different

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tags you can see all the way up to seven

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then when I push it again so 1 2 4 5 6 7

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is going to remove all of those except

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from number three which is The Hourglass

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so if for example I say you know what

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I've read all of these that was holding

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shift on my keyboard and clicking I can

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push three to say I'm not waiting

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because I'm going to push two and say

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actually I'm done so let's go in and

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just actually highlight something so it

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I have actually done something yep look

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there we go some really important

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highlighted stuff and let's just grab

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some red ones in there as well well

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that's obviously really important

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because I know exactly what I'm doing

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then we jump back to obsidian I go

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command

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pallet Danny import find the paper so

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long-term Flyn effect enter enter and

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you can see it's appeared inside of the

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folder and there we have all of our

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really awful highlights but they're

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there you can see that one's a red

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highlight that one's a yellow highlight

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and you can separate all of these out in

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loads of different custom ways but I

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just want it in here to start with and

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now I want to write my essay well I'm

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going to remove all of these words

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because I don't need those and how I set

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this out is I make a sources heading so

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this is a heading one with a hash and

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then I go hash and then script then I

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make a heading two so hash

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space

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list hash

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space

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points then if I go to the top right and

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click on the expand button then gives me

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the these four different options and I

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want the outline so it's going to show

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all of those headings and I can navigate

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up and down the file and where obsidian

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gets really cool is you can link inside

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of obsidian so if I go to points and I

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go square bracket square bracket it

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brings up a list of all of the files in

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my obsidian Vault folder so if I go dton

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there's that datton paper and if I go

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

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are both Linked In ins side of the file

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why is that important well if I right

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click on the tab and pin it now this

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essay tab is going to stay where it is

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if I click on this it opens up the file

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and again if I drag this over I now have

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a split screen so I can click on that

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Source there's the source and there's

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the other source so I can go between all

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the different sources and bring in the

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points I think are relevant so let's

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just create some space this point is

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important so contrl Ctrl V uh this point

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is important crl c contrl v and uh this

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image is actually really important so

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I'm going to crl C and then drag that

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down crl V now that was the Dutton paper

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so if I copy that and then paste that

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link underneath this point so I know

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where it comes from this point so I know

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where it comes from and this table so I

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know where it's come from I can get rid

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of that link control D and now I'm going

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to go to this next source uh this point

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is actually related to this point so I'm

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going to paste that underneath and this

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point is actually related to this table

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so I'm going to paste that underneath

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now I'm seeing a trend here so I'm going

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to

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make a heading of topic one and this is

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actually going to be another heading of

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topic two so I'm going to copy that

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paste underneath that point and paste it

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underneath that point remove the Source

play14:59

at the top so now I have the links going

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from the source to the highlighted point

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and they go back to zoto if I now come

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to this source file and click on the

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back Links panel you can see it's linked

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to the essay and it's showing I have two

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points that are linked there I can

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expand it and it shows me what's linked

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if I go to the essay file and go to the

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outgoing links you can see they are the

play15:22

two sources that I've linked plus the

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image file now I'm writing my essay well

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I want to start writing it but I don't

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to have to scroll up and down because

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obviously that's just inconvenient so

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what I can do is I can rightclick and

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then go split to right so now I have the

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essay file open twice and going to close

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down this tab that was middle click with

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

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open up the outline again go down to the

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script and say introduction now in the

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introduction I want to write about topic

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one

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so I'm writing something really

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important and that is this reference so

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I can copy and then just paste it right

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in there so I know okay this point was

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referenced here now what I tend to do is

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actually delete this because I now don't

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need this point anymore so I get rid of

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that so my points list disappears

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because I know I've processed it and

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started writing about it you may want to

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keep them together I personally don't

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now here you can see we've got two

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points that are the same or related in

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some way I haven't actually read these

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so they're probably not but maybe I want

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to paraphrase both of these and say this

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is good IQ stuff that's the word IQ from

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there and then different countries there

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just different countries from here and I

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want to reference both of them well I

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can just go

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copy paste and then in here I go copy

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and paste so now I've got the two

play16:53

different sources referencing one point

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uh now I don't need these anymore so I

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can just delete all of those then I can

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cut it from here and then paste it

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underneath here this is slowly starting

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to build out but now let's just say I

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want to have a conclusion of course I

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need to map out all the other sections

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as well so we've got our literature

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review we got a results we've got a

play17:18

discussion so we can jump backwards and

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forwards to any point of those documents

play17:22

let's go down to the conclusion so this

play17:24

table has some interesting points maybe

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you want to say something about that so

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the Flint effect was in lots of

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countries so I copy there paste there so

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now I've got the source I can copy paste

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it into the result so these are some

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results maybe it's part of your lit

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review so let's just X and then paste so

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those crl X to cut contrl V to paste now

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I don't need it inside of here so I can

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get rid of that get rid of those and for

play17:49

the conclusion actually you know what I

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like this but I'm not entirely sure what

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this was talking about so I'm going to

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click on the page one take me okay

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that's what it was talking about I

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remember remember now it was something

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to do with this thing I don't know I'm

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making this up so I come back then I can

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say whatever it is that I want to say

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about this thing in the conclusion we

play18:08

are getting Dumber because that's what

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the reverse flim effect is about

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basically you know what I want to leave

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this there cuz I might add this into the

play18:15

discussion but I'm not sure so I'm just

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going to leave that there just in case

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now I have my essay written out in

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obsidian with links back to the

play18:22

appropriate sources as I write and as I

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think maybe I go oh actually you know

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what if I go in into this file so you

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can see I've opened the source file

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straight away I can see oh this was

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tagged with something or oh yeah I had

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this idea I may want to add that to the

play18:38

script well I've got the sa file open

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over here so I can add it to the results

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but maybe it was actually appropriate in

play18:44

the discussion so this this comment here

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that I made actually this came up with

play18:48

this idea in the discussion point so I'm

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going to get rid of that one again

play18:52

middle click on the mouse and you can

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see it's inside of the discussion

play18:55

section so you can write and think at

play18:57

the same time going backwards and

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forwards between different pages again

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you can have tabs you can have multiple

play19:04

splits so you can have it top down the

play19:06

bottom you can show or hide anything and

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it just makes the writing and thinking

play19:11

space much cleaner for me however if you

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want to turn it into the university well

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that's where you're going to have to

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take it out of markdown out of obsidian

play19:20

and into Microsoft Word so going to go

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settings Community plugins and browse

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going to go with pandoc

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install enable options and you'll want

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to make sure you've got pandoc installed

play19:34

on your device so type pandoc into

play19:36

whatever browser you use download the

play19:39

latest version so go to the download

play19:41

page and then download it I'm on windows

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so I'll download one of these and then

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if you're on Mac you download that Linux

play19:46

ET etc etc but once that's all

play19:49

downloaded you can see you can change

play19:50

the internal links so that's these

play19:52

things at the moment they've got two

play19:54

brackets

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on you can change those so it turns into

play19:58

text text and if I open up that left

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side barar you see we're in the folder

play20:02

this one is the essay file if I close

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this down this is the essay file if I go

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to that command pallet button again

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search for pandoc I've just typed in pan

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for short and then word I'm now going to

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use the pandoc plugin to export as a

play20:17

Word document you see exporting and

play20:19

successfully exported so it is now

play20:21

inside of these folders but we can't see

play20:24

it go down to settings files and links

play20:27

now I want to detect all file extensions

play20:29

because it's been changed to a docx file

play20:32

and there it is so when I click it I

play20:34

already have a saved Word document that

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was on my other screen here so it's

play20:39

brought in the headers it's brought in

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the links and you still I've still got

play20:42

the link back to Zer if I want it but

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there is the script this is where if you

play20:46

want this to be automatically cited

play20:49

properly then you can use pandoc

play20:51

information with bibliography files and

play20:53

CSL files or if you've already got it

play20:55

linked with zoto you've got your word

play20:57

linked with zoto you can say okay I need

play20:59

to add a citation this is the Dutton

play21:03

citation so add I'm going to use Harvard

play21:05

elevia okay let's just type in dton the

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negative Flint effect that's the one

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let's go enter and now it's been added

play21:12

in so I can get rid of that come down to

play21:15

the bottom and then go edit and add

play21:17

bibliography now I've added the duton

play21:20

bibliography if I was to then copy that

play21:23

and then let's paste it in there because

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that's there as well but we also need

play21:28

this citation so I come on to there

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let's say add or edit cuz I copied the

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

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what's that te's yeah there we go so

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enter now I've got the two different

play21:41

citations I push enter and it's got

play21:44

bigger because it's now added the two

play21:45

different citations in so we can get rid

play21:47

of that bit from word but now the

play21:50

bibliography has extended so we've got

play21:52

the tside at the top of the other file

play21:54

so zoto and word working together this

play21:56

is how I would do it to make sure

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nothing is missed if you were to do it

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automatically of course something could

play22:02

get missed so I would copy and

play22:05

then backspace paste just to make sure

play22:08

that all the citations are in

play22:09

appropriately in the formatting that you

play22:10

want but the main point here for me is

play22:13

with obsidian you can have the same file

play22:15

open twice so the essay open twice or

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you can have sources open go through

play22:18

sources you can essentially puzzle make

play22:21

all of the different points into the

play22:23

script with whatever outline you have or

play22:25

whatever running Theory concept idea

play22:28

philosophy value that you're working

play22:30

with you can see all of the words at the

play22:32

same time and it doesn't have to be one

play22:34

big long document on word that you're

play22:36

scrolling up and down or you're clicking

play22:38

outline to navigate through this for me

play22:40

Works obviously everyone is a little

play22:42

different