Video summary

How I Use ObsidianMD and Zotero For Academic Research

Main summary

Key takeaways

Educational

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)

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

Original video