Academic Note Taking and Making System [with The Zettelkasten Method - Obsidian - Zotero]

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CENTRAL
CENTRAL1920×1726 126 KB

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Important Disclosure: The information provided in the flow diagram below is based on over 100 YouTube videos and some articles on the internet. For this reason, some sentences are quoted and cannot be identified because the sources are mixed together. Apart from that, this system between Obsidian and Zotero is built from scratch, but the Nunjucks templates used in the system are edited with templates shared on the internet and Nunjucks documentation. Links to the playlists of all the videos watched and links to the articles will be shared, some of them I may not be able to share if I haven’t saved them.

Note System Scheme
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You can view this image in high quality: Note System Scheme.png - Google Drive

01 Literature Sources

  • The source of notes transferred from Zotero is saved. This reduces dependency on Zotero and also keeps a record of information to be used when citing. This makes it easy to find the source if one wants to return to the source from which the note was taken.
  • Notes highlighted in the literature can be imported into Obsidian from the following sources (a single template has been created that can save them all for import):
    • Article
    • Thesis
    • Book or book chapter

[!caution] Importing from Zotero can be done many times.

  • No metadata (front-matter) should be saved manually.
  • Saving source information, relationships with other sources in Zotero and manually adding notes (not through highlighting) to sources in Zotero are only done in Zotero. These changes made in Zotero are imported and saved with the Zotero Integration plugin.

01 Literature Source Template.md (2.0 KB)

---
tags: [01-literature-source]
cssclass: 01-literature-source
file-class: [_01-literature-source_file-class]
citekey: {{citekey}}
source-type: {{itemType}}
title: "{{title}}"
{%- for type, creators in creators | groupby("creatorType") -%}{% if loop.first %}
{% endif %}{{type | replace("interviewee", "author") | replace("director", "author") | replace("presenter", "author") | replace("podcaster", "author") | replace("programmer", "author") | replace("cartographer", "author") | replace("inventor", "author") | replace("sponsor", "author")  | replace("performer", "author") | replace("artist", "author")}}s: "{%- for creator in creators -%}{%- if creator.name %}{{creator.name}}{%- else %}{{creator.lastName}}, {{creator.firstName}}{%- endif %}{% if not loop.last %}; {% endif %}{% endfor %}"{% if not loop.last %}
{% endif %}{%- endfor %}
publicationTitle: "{{publicationTitle}}"
publisher: {% if publisher %}"{{publisher}}"{% endif %}
url: {{url}}
date: {{date | format("YYYY-MM-DD")}}
year: {{date | format("YYYY")}}
isbn: {% if ISBN %}{{ISBN}}{% endif %}
issn: {% if ISSN %}{{ISSN}}{% endif %}
language: {{language}}
edition: {{edition}}
volume: {{volume}}
issue: {{issue}}
---
# Navigation
fleeting-note:: [[02FN {{citekey}}]] ➡️
literature-note:: [[03LN {{citekey}}]] ➡️➡️
___
tags::
{%- if tags.length > 0 -%}
{% for t in tags %} #{{t.tag | lower | replace(" ", "-")}} {% endfor %}
{%- endif %}
___
> [!info]- Bibliography
> {{bibliography}}
> 
>> [online]({{uri}}) [local]({{desktopURI}}) {%- for attachment in attachments | filterby("path", "endswith", ".pdf") %} [pdf](file://{{attachment.path | replace(" ", "%20")}}){% if loop.last %} {% endif %}{%- endfor %}

> [!abstract]- Abstract
> {{abstractNote}}

___
# Related with other literature sources
{% if relations.length > 0 %}
{%- for relation in relations %}- [[01LS {{relation.citekey}}]] 
{% endfor %}
{%- endif %}
# Special comments about this literature source
{% if notes.length > 0 %}
{%- for note in notes | reverse %}comment:: {{note.note}} 
{% endfor %}
{%- endif %}

02 Fleeting Notes

[!question] What is it? (In general use)

  • These can be spontaneous thoughts and ideas that are scribbled (jotted) down immediately, so as not to forget them for later reference.
  • “Fleeting Notes are like "reminders of knowledge ".” ~ Sonke Ahrens, How to Take Smart Notes
  • At this early stage, there is no need to be conditioned to write complete sentences.
  • It is like little scratch notes (jottings) taken quickly.
  • What matters is what we do with the instant notes when we come back to them later.

What is it? (In this system that design for academic note generation)

Highlighted notes from Zotero are imported.

[!caution] Importing from Zotero can be done many times. BUT!

  • Only edits to tags must be made from Zotero, otherwise the next import will delete the maually (handwritten) tags and replace them with whatever is stored in Zotero.
    Manual changes to notes in Obsidian that were previously imported will remain. Changes made in Zotero after the most recent import will be added at the end (under the import date heading). The same applies to manual changes made in Obsidian to a note previously highlighted in highlighter in Zotero and imported into Obsidian.

[!attention] Primary Source
Information in secondary sources should only be made into a literature note when the primary source is unavailable.

[!todo] “Cited In” Information

  • When marking the information from the secondary source with a highlighter, include the parenthesis at the end of the sentence (the parenthesis where the author cites the source). In addition, this primary source in the author’s citation should be marked with a highlighter in the bibliography.
  • " - [ ] ‘task-tag’ " (Ctrl + L (Windows) or Cmd + L (Mac)) at the beginning of the source to make it a task list to go to and read the primary source. This way all the resources that need to be accessed to the primary resource can be seen and managed on one page (with the Tasks community plugin).
  • The primary sources can be searched first with the "Reference Map " community plugin, and if not found there, they can be searched in electronic libraries.

02 Fleeting Note Template.md (1.5 KB)

---
tags: [02-fleeting-note]
cssclass: 02-fleeting-note
file-class: [_02-fleeting-note_file-class]
---
# Navigation
literature-note:: [[03LN {{citekey}}]] ➡️
literature-source:: [[01LS {{citekey}}]] ⬅
___
tags:: 
{%- if tags.length > 0 -%}
{% for t in tags %} #{{t.tag | lower | replace(" ", "-")}} {% endfor %}
{%- endif %}
___
> [!info]- Bibliography
> {{bibliography}}
> 
>> [online]({{uri}}) [local]({{desktopURI}}) {%- for attachment in attachments | filterby("path", "endswith", ".pdf") %} [pdf](file://{{attachment.path | replace(" ", "%20")}}){% if loop.last %} {% endif %}{%- endfor %}

> [!abstract]- Abstract
> {{abstractNote}}
___

{% persist "annotations" -%}
{% set annotations = annotations | filterby("date", "dateafter", lastImportDate) %}
{% if annotations.length > 0 %}

# Imported on {{importDate | format("YYYY-MM-DD hh.mm a")}}

{%- for annotation in annotations -%}

{% if annotation.imageRelativePath %}
![[{{annotation.imageRelativePath}}]]
{% endif %}

{% if annotation.annotatedText -%}
**{{annotation.annotatedText}}**
{%- endif %}
{% if annotation.comment -%}
{{annotation.comment}}
{%- endif %}
tags::{% if annotation.tags %}{% for tag in annotation.tags %} #{{tag.tag}} {% endfor %}{%- endif %}
[Open in Zotero (p. {{annotation.pageLabel}})](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.pageLabel}}&annotation={{annotation.id}}) Imported on {{importDate | format("YYYY-MM-DD h:mm a")}}
___
{%- endfor %}
{% endif %}  
{% endpersist %}

03 Literature Notes

[!question] What is it? (In common use)

  • These notes are summaries of your thoughts specific to a text.
  • They are summaries of what we understand from consumed content (articles, theses, books, etc.).
  • A literature note is tightly linked to the source material. However, they are not permanent notes.
  • While these notes are meaningful in the context in which they come from, in making permanent notes out of them, these permanent notes should be understandable when read in isolation.

What is it? (In this system that design for academic note generation)

  • These notes are written not atomic, organized under headings. Thus, when linking to the source of the Permanent Notes, they can be linked through these headings. Since these notes have not yet been isolated (stripped) from the context of the source, they are collectively kept in a single note, preserving the integrity of the context.

[!info] One important point where this system differs from the original…

  • Normally, Literature Notes are made atomically and decontextualized (like Permanent Notes), and the useful notes from them are saved as a copy of a Permanent Note, or are themselves saved as a Permanent Note and linked and related to other Permanent Notes. In this case, the process of making a Permanent Note is sorting (selecting) the Permanent Notes from the Literature Notes and connecting them with other Permanent Notes. In this way, only those that have a plus to their existing notes become permanent notes.
  • Keeping the same plus, in this system, Literature Note will not be made atomic, but will instead be a single note grouped under a heading, so that all the notes from one work are in a collective form, keeping the context. This will make it more understandable when referring back to the Literature Note.

[!question] Why would one need to go back to the Literature Note?
If the Permanent Note is not understandable when read after a long time and needs the context of the Literature Note from which it is sourced, there may be a need to go back to that Literature Note).

  • In this case, the process of making a Permanent Note is to write Permanent Notes in an atomic form, by decontextualizing the ideas in the Literature Note from the context of the Literature Note, and associating them with other Permanent Notes.
  • Not everything in a Literature Note has to be made into a Permanent Note. Only those that add to the existing notes, meaning those that add to the existing body of knowledge are made into a Permanent Note.
  • Literature Notes created by translating the explanation or definition of some concepts from a foreign language are tagged with the tag “citable”, which means “The information in this Literature Note can be used directly by citing it”. These notes are not included in Permanent Notes because they are not our own thought, but a translation of another author’s thought into our own language.
  • If the source of the information is stated as cited, meaning that a secondary source has to be used, the APA style inline citation (as-cited-in) is placed at the end of this information. Citation can be added with the “Zotero Integration” community plugin.

[!attention] How should I link to permanent notes?
Literature Note should not link to Permanent Notes. When Permanent Notes are created, under the “References” heading, link to the Literature Notes that are sources for the Permanent Note ( it becomes a Permanent Note.) or link to the Permanent Notes that are sources for the Permanent Note (it becomes a Meta-Permanent Note.).

03 Literature Note Template.md (287 Bytes)

---
tags: [03-literature-note]
cssclass: 03-literature-note
file-class: [_03-literature-note_file-class]
---
status:: #status/backlog
___
# Navigation
fleeting-note:: [[02FN {{VALUE:citekey}}]] ⬅
literature-source:: [[01LS {{VALUE:citekey}}]] ⬅⬅
___
tags:: 
___
# Literature Note

04 Permanent Notes

  • Written in complete sentences and in your own words.
  • Add only single idea (thought) per note (card). Thus, it is easier to discover new ideas and make connections between notes.
  • The important point is that Permanent Notes are not a summary of the source, but a context-free (uncontextualized) thought generated from the source.
  • Permanent Notes, are written in a way that can still be understood even when you have forgotten the context they are taken from.” ~ Sonke Ahrens, How to Take Smart Notes {Thus, easy to understand in isolation.}
  • Remember, the Permanent Notes are moving the Literature Note from the context of a single source material (e.g. a book) to your whole collection of knowledge (from all books, articles, etc). Like a jigsaw puzzle, you are taking this new piece and slotting it in where it fits.
  • Literature Notes are author’s understanding while Permanent Notes are your insight, your understanding.

[!tip] Use Aliases
Use aliases metadata for adding extra names to the note, aliases could be maybe English version of the note title or alternative name of the note title.

[!important] Meta-Permanent Notes

  • The source of Permanent Notes is Literature Notes, while the source of Meta-Permanent Notes is Permanent Notes. (such as Higher-Order Conditioning (Second-Order Conditioning))
  • Meta-Permanent Notes only add the “meta-permanent-note” tag to the Metadata section (Front-matter, YAML, Properties) of the Permanent Notes. So that you can quickly filter between Permanent Notes and Meta-Permanent Notes.

04 Permanent Note Template.md (337 Bytes)

---
tags: [04-permanent-note]
cssclass: 04-permanent-note
file-class: [_04-permanent-note_file-class]
aliases: 
 - ""
---
# Navigation
up-MOC:: 
___
tags:: 
___
# Permanent Note

# References

# Related
## Where this idea comes from? 

## What is similar to this idea? 

## What is opposite of this idea? 

## Where this idea leads to?

Go on a joyful discovery…

[!question] Ask yourself these questions…

  • Do I have an already existing note on this topic?
  • Does it add a new understanding or thought to what you already have?
  • Does it change your understanding of any existing notes?

[!todo] Explore
Review your notes and think about what gaps, ideas and connections could be made.

[!check] Use tags to categorize.
If there is a specific theme, tags can be added to find the note easily.

[!caution] Don’t over-tag.
Over-tagging makes it harder to find, filter and distinguish notes, contrary to the benefit of tagging.

[!check] Connect your thoughts using MOC (Maps of Content).
Are there any notes that are related and add more information if you add a link to this new note?
If so, link between related notes and between these notes and an existing MOC or a new MOC.

[!tip] A note can be associated with more than one MOC.
Relationships can be established with the "up-MOC " metadata in Permanent Notes, or with wiki-link under the "Related " heading.

05 Maps of Content Template.md (134 Bytes)

---
tags: [05-MOC]
cssclass: 05-MOC
file-class: [_05-MOC_file-class]
aliases: 
 - ""
---
# Navigation
up-MOC:: 
___
tags:: 
___
# H1

Create understanding…

[!example] Example
Note 1 has a wiki-link to Note 2.
Note 2 has a wiki-link to Note 1.
…
Note 3 has wiki-link to Note 1 and Note 2.
=> Note 1 + Note 2 + … = Note 3 (A new insight note)

[!caution] Don’t add links (wiki-link) to every keyword

  • If the two persistent notes are really related, you can link through this keyword (wiki-link) or you can add links directly at the bottom of the note.
  • When linking, make sure you can explain the link you are linking to. Don’t make a link you can’t explain, don’t add a link.

Create your own works

Create a new MOC for the new work. Then, using wiki-links, collect all notes that can be used in the work under the related subject headings.

[!check] Create a project
Create a project for the new work, prepare tasks to be done in the work and manage these tasks with the Tasks community plugin.

Obsidian Zettelkasten Template Vault and Settings Link:

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