System Overview

Get to the system; the rest is just fun notes.

Initial Configuration

  • Set up an account on Zotero for sync

  • Install Zotero and Better BibTex on your machine

  • Install Zotero plugin in Obsidian

  • Create a template note for Obsidian + Zotero integration

    • I have it grab the annotations and notes and insert them into the document

    • My template is at the very bottom

  • Update Zotero plugin in Obsidian with the import note formatting option to reference the template, and where to place the note.

Taking Notes

  • Take notes in Zotero itself.

    • Use markdown formatting and use [[ ]] around where you typically would be linking to a page.

    • Don't worry about it being right. The goal is to ensure that you get the notes done, NOT that Obsidian is perfect!

  • Do not take notes in Obsidian. This is an ADHD trap! STAY AWAY!

  • For PDFs, I annotate in Zotero using the comments sticky notes.

  • For textbooks, I add a note per chapter and start with heading 2 as top level. This is because I have Notes as the top level heading in my Zotero Source Template.

  • For digital sources, including textbooks, I have Obsidian closed and split screen with Zotero on one side, and the digital source on the other.

    • DO NOT OPEN OBSIDIAN! ADHD BEACON OF DISTRACTION! NO!

  • If you need to take a note of something that isn't in the source, and would be something better written down, then use a notepad to get a starting structure.

    • I find this is better for tables where I'm comparing different ideas/objects with their parameters (*check whiteboard)

Syncing Notes

  • When I'm done taking notes for now, I open up Obsidian, and choose Zotero Integration: Source Imports Template

    • Choose your source in either the search view, or Classic view

  • Tah-dah! You now have a markdown notes that can link everywhere without having gotten distracted the whole time!

Bonus: Log

  • Since I also use Obsidian as a logbook, I create a new note with PARA type resource, object type log with the date. Add in the notes of what I worked on that's associated to a project. E.g. "2025-10-13 - Research Paper Log" and note what I did for the research paper (e.g. - notes in Zotero and synced. Started on section A, ended at section B. Created notes C, D)

Basic Object Focused Knowledge Structure

This past week I wanted to share some information around a security system, so I used my trusty whiteboard to draft the information. In order to make it easier for others to understand my annotations, and so I remember how to keep it consistent, I set up my whiteboard with whiteboard tape to section off a title, and a reference section on the left side. I use a framework of objects that encompasses both physical objects (e.g. a galaxy), and abstract objects (e.g. a definition, equation, theory, etc.) so that summary is there as well.

a whiteboard that is split into different sections to server as a reference to my approach for knowledge and annotations. 1. properties of objects - parameters (object specific) that can either be physical (e.g. radius of the sun), or abstract (e.g. classification, etc.) - inheritance tree that can have child object(s) or parent object(s) - relationships that can be concepts (e.g. mass sequence of components of galaxies), theory (including transformers / equations), or systems (e.g. workflows) 2. Reference Key provides a visual reference for annotations of a: - note (with a dash) or a subnote (hanging indent with a dash) - concept/context that has cloud-like squiggly underline - object (including theory/system) that is a regular underline - main topic that is a double underline - flow directions with arrows that can me that the item leads to another (arrow points away), the item is because of something else (arrow points towards), or a bi-directional relationship (both ends of a line have pointy arrows) 4. System Diagrams System diagrams, workflow diagrams, or relationship diagrams have different symbols that can reflect the objects. - A transformer is denoted by a cloud - A decision is denoted by a diamond - a collection is denoted by a dashed ring around the objects - an object can be anything (will have a legend) and shows examples of lines around a circle, a box, a box with a checkmark, a circle, and a circle with a checkmark - flow indicators: lists the three types of arrows as listed in the flow directions of 2. Reference Key

I bring this up as I then spent a bit of time organizing how I would like this better reflected in Obsidian, a tool I've been using off and on for years for knowledge management. I love the connected nature of the notes, and often I'm working on topics that are related over years of study, or years of evolution of a technical topic. Treating knowledge in an object-oriented way feels like programming, and I can set up a logical system to assist with this.

Where Zotero Comes In

Oddly, installing random software on work machines isn't something I recommend (/end sarcasm). A challenge I have had with getting lessons learned from the public domain into Obsidian is the integration of notes afterwards. I stared in automation as I struggle to perform routine tasks, so I was looking for a way to add reference notes to Obsidian with full citation setup for articles, podcasts, or documentation that is in the public domain. I need a way to segregate the contents of the source from the thoughts I have on the material.

Zotero (https://www.zotero.org) has a handy website where you can add and check the references online. While I'm typically using the app on my personal devices, this gives a good compromise for adding better references for what I'm learning, and an opportunity to rewrite the material as a paraphrase or summary helping solidify my learning. Bonus, not plagiarizing so I can give credit where it's due while accurately representing the source material.

Obsidian's Strength

Since I'm typically talking to people, it's nice to be able to search for a source quickly. Since I love learning, I want a system where I can expand upon my ideas while referencing the sources notes. Obsidian (https://obsidian.md) is perfect for both of those, and you can see the structure form with graph view.

The flexibility of the system is also why I created a note called "Guide - How To Use This Obsidian Vault." This acts as a reference for how I configured Obsidian, and will add a log each time I make a change/decision.

A brief summary of my structure is below:

a whiteboard with "Obsidian Vault Reference" that structures PARA tags (Building a Second Brain - Projects, Areas, Resources, Archive), Object Type tags (source, note, reference, idea, question, event, main) Along with a task of to-do's (detail the PMK system, create templates for new note/daily note/new resource/new project), and pages for top level vault (inbox, current projects, next actions, resources, areas, my notation reference doc)

Obsidian Template for Zotero Sources

The following is my template for Zotero sources, which expands upon the initial documentation from the plugin: https://github.com/mgmeyers/obsidian-zotero-integration/blob/main/docs/Templating.md

%%
Zotero documents are overwritten with the Zotero database contents. 
To change the output in this document, update the Zotero note for this 
reference source. 
%%
# Formatted Bibliography
{{bibliography}}

{% if abstractNote %}
# Abstract
{{abstractNote}}
{% endif %}

# Annotations
{% for annotation in annotations %}
{% if annotation.annotatedText %}
{{annotation.annotatedText}}
{% endif %}
{% if annotation.comment %}
{{annotation.colorCategory}} - {{annotation.date}}
{{annotation.comment}} (p. {{annotation.pageLabel}})
{% endif %}
{% endfor %}

# Notes
{% for note in notes %}
{{note.note}}
{% endfor %}