Summary of "How I Use ObsidianMD and Zotero For Academic Research"

High-level summary

The video demonstrates a practical, no-code workflow for using Zotero and Obsidian together to manage academic literature, take literature notes, and plan reading. The presenter emphasizes a simple, robust setup that avoids coding and duplication: Zotero is the single source of truth for PDFs and highlights, and Obsidian is used for linking and synthesizing notes.

Core aims: - Reduce duplication of files and metadata. - Make notes and citations linkable and future-proof. - Reveal connections between papers via Obsidian backlinks and graph view. - Build an evolving reading and note-taking system.

Main concepts and lessons

Keep Zotero as the canonical repository for bibliographic metadata and PDFs. Use Zotfile to move PDFs to a tablet for annotation and sync them back.
Use Better BibTeX (BBT) in Zotero to generate stable citation keys in a consistent format and mirror that format in Obsidian so links work automatically.
Export the Zotero library (Better BibTeX export) into your Obsidian vault and keep the export updated so the Obsidian Citations plugin can search it.
Use the Obsidian Citations plugin to create literature notes from Zotero entries via a template. Use the citation key as the note title so manual in-text-style citations (e.g., walker2011) automatically link to notes or create placeholders.
Use Obsidian backlinks and graph view to visualize relationships between papers and to prioritize reading (e.g., papers cited by multiple items you’ve already read).
Keep the setup minimal and visual: a tag/status system (emojis), a simple folder for literature notes, a clean template, and a readable theme.
This workflow requires no coding — it relies on Obsidian community/core plugins only.

Detailed workflow (step-by-step)

Zotero setup
- Install Zotero and add these plugins:
  - Better BibTeX (BBT) — for consistent citation keys and export.
  - Zotfile — to send PDFs to a tablet for annotation and to sync annotated PDFs back to Zotero.
- Configure Better BibTeX citation key format. Example formats the presenter uses:
  - Single author: authorLastName.year (e.g., walker2011)
  - Two authors: author1.author2.year (dot-separated)
  - More than two authors: firstAuthor.l.year (first author + l + year)
  - Choose a format that is easy to type and resembles in-text citations.
- Annotate PDFs on an iPad (PDF Expert was used in the video) and ensure annotated PDFs return to Zotero so highlights/notes live in one place.
- Use one Zotero folder as an “inbox” for quick citations to be processed later.
Export Zotero for Obsidian
- In Zotero: File → Export Library → choose Better BibTeX exporter and check “Keep updated”.
- Save the exported file into your Obsidian vault (for example, inside a zotero folder in your PhD vault).
- The exported BBT file is what the Obsidian Citations plugin reads.
Obsidian setup (no coding)
- Install Obsidian and the necessary community/core plugins (avoid GitHub plugins if you want to keep it simple).
- Install and configure the Citations plugin:
  - Point it to the exported BBT file inside your vault.
  - Configure a folder where literature notes will be created (e.g., Literature Notes).
  - Set a hotkey for the citation search/creation command.
- Theme and appearance:
  - The presenter uses the Minimal theme + Style Settings plugin.
  - Customize accent color and set italics to a standout color so personal thoughts vs. quoted content are visually distinct.
Create and use a literature note template
- Template fields (example):
  - Title: use the citation key (BBT key) as the note filename/title.
  - Metadata block: actual paper title, authors, year, link to Zotero entry, status emoji (orange = unread, green = read, red = DNF), tags.
  - Sections/headings: Abstract (short summary), Notes (quotes, thoughts; include page numbers for quotes), References to check out (other cited works to consider reading).
  - A short block for “how it’s relevant to me” or similar personal context.
- Use the Citations plugin hotkey to search the exported Zotero library and create a new literature note from the template; it auto-populates bibliographic metadata.
Linking and future-proofing citations
- While reading, type the citation key inside double square brackets, e.g., [[authorYear]], to create an internal Obsidian link.
  - If the literature note exists, the link connects to it.
  - If it doesn’t exist, Obsidian creates a placeholder note that will link automatically once you generate the full note later.
- This ensures links added while reading are consistent and will be resolved later.
- Use backlinks in each note to see which other notes cite or are cited by the current note.
Using graph view and backlinks for discovery and planning
- Graph view shows nodes for literature notes (presenter colors them to distinguish states).
- Inspect nodes to see which notes cite the same article.
- Prioritize reading by identifying papers cited by multiple items you’ve already read — add those to a reading list.
- Use local graph view (limited depth) on a single note to explore its immediate citation neighborhood and decide follow-up readings.
Tagging and status management
- Use emojis or tags to reflect status:
  - Orange = unread
  - Red = DNF (did not finish)
  - Green = finished
  - Other emojis (leaves, nuts) to indicate importance or further work needed
- Be liberal with tags early on — avoid over-optimizing tagging at the start.
Keep everything centralized and avoid duplication
- Zotero = source of PDFs and metadata. Obsidian = synthesized, linked notes.
- Avoid multiple copies of the same PDF across apps (previous workflows with GoodNotes/OneNote caused duplication).
- Use Zotfile to ensure annotated PDFs return to Zotero.

Plugins, tools, and extras mentioned

Zotero (bibliography manager)
Better BibTeX (Zotero plugin) — for stable citation keys and export
Zotfile (Zotero plugin) — for extracting/sending PDFs to tablet and syncing annotations
PDF Expert (iPad PDF annotator) — used for annotation
GoodNotes, OneNote (mentioned as previous approaches to avoid)
Obsidian (note-taking knowledge base)
Obsidian Citations plugin — key plugin for generating notes from Zotero export
Minimal theme and Style Settings plugin (appearance)
Obsidian graph view and backlinks (built-in visualization/core features)
Obsidian community plugins / Discord / forums (resources)

Practical tips and reminders

You don’t need to use coding or GitHub to build a powerful Obsidian + Zotero workflow; community plugins and simple templates/key formats are enough.
Make citation keys easy to type and consistent between Zotero and Obsidian to enable quick, manual linking as you read.
Keep the Zotero export in your vault up to date so the Citations plugin can search and create notes reliably.
Record page numbers for direct quotes so you can find the original text quickly.
Use the graph and backlink views actively to reveal influential or central papers and guide further reading.

Limitations and things to expect

The system is evolving — expect to iterate and refine the workflow.
Graphs can become visually noisy; tweak filters and local graph settings to manage complexity.
Some setup is required (install/configure plugins and template), but no programming skills are necessary.

Speakers and sources

Video presenter (unnamed) — walks through the workflow.
“Holly” — livestream host whose session inspired the video.
Tools/plugins referenced: Zotero, Better BibTeX, Zotfile, PDF Expert, GoodNotes, OneNote, Obsidian (Citations plugin, Minimal theme, Style Settings), Obsidian community/Discord/forums.