brycewang-stanford/obsidian-citation-guide

Obsidian Citation Guide

A skill for using the Obsidian Citation Plugin to integrate bibliographic references from BibTeX or CSL-JSON files into the Obsidian knowledge management workflow. Based on obsidian-citation-plugin (1K stars), this skill enables researchers to create literature notes, insert citations, and build interconnected knowledge bases grounded in their reference libraries.

Overview

Academic researchers need their notes to be deeply connected to their references. The Obsidian Citation Plugin bridges BibTeX or CSL-JSON bibliography files with Obsidian's note-taking system, enabling seamless creation of literature notes from reference entries, quick citation insertion while writing, and automatic backlinking between notes and their source references.

Unlike Zotero-specific integrations, this plugin works with any tool that exports standard BibTeX or CSL-JSON, making it compatible with Zotero, JabRef, Mendeley, EndNote, and even hand-crafted .bib files.

Setup and Configuration

Prerequisites

• Obsidian with community plugins enabled
• A BibTeX (.bib) or CSL-JSON (.json) bibliography file
• The bibliography file should be accessible from the Obsidian vault directory

Installation

• Open Obsidian Settings and navigate to Community Plugins
• Search for "Citations" in the plugin browser
• Install the Citations plugin and enable it
• Navigate to the plugin settings to configure your bibliography source

Configuration

• Set the path to your .bib or .json bibliography file
• Configure the literature note folder (e.g., references/ or literature/)
• Set the literature note template with desired frontmatter fields
• Define the citation format for in-text insertions
• Configure the citation key format used for note file names

Template Variables

• {{citekey}} - the unique citation key for the reference
• {{title}} - the full title of the work
• {{authorString}} - formatted author list
• {{year}} - publication year
• {{abstract}} - the abstract if available in the bibliography
• {{DOI}} - Digital Object Identifier
• {{URL}} - web link to the publication
• {{containerTitle}} - journal or conference name
• {{page}} - page numbers
• {{tags}} - keywords or tags from the bibliography entry

Core Workflows

Creating Literature Notes

• Use the command palette to open the citation picker
• Search by author, title, year, or any metadata field
• Select a reference to create a new literature note from the template
• The note is populated with metadata from the bibliography entry
• Add your own annotations, summaries, and connections to the note

Inserting Citations

• While writing in any Obsidian note, trigger the citation insertion command
• Search and select the desired reference
• The citation is inserted in the configured format (e.g., [@citekey], [[@citekey]])
• Citations create automatic backlinks to the corresponding literature notes
• Multiple citation formats can be configured for different output targets

Browsing References

• Open the citation panel to browse your entire bibliography
• Filter by type (article, book, chapter, conference), year, or author
• Preview reference details without creating a note
• Quickly jump to existing literature notes for any reference
• Identify references that do not yet have corresponding notes

Literature Note Strategies

Minimal Notes (Quick Reference)

• Include only the frontmatter metadata (citekey, title, authors, year)
• Add a single-paragraph summary of the paper's contribution
• Tag with 2-3 topic tags for filtering
• Useful for references that provide supporting context but are not central to your work

Standard Notes (Working Knowledge)

• Include full metadata frontmatter
• Add sections for: summary, key findings, methodology, strengths, limitations
• Extract 3-5 key quotes with page references
• Link to related literature notes and concept notes
• Tag with topic, method, and status tags

Deep Notes (Core References)

• Include everything from standard notes plus:
• Detailed methodology breakdown with your assessment
• Figure and table descriptions with your interpretation
• Questions and ideas prompted by the paper
• Connections to your own research with specific implications
• Reading timeline notes tracking your evolving understanding

Building a Connected Knowledge Base

Linking Strategies

• Link literature notes to concept notes that represent key ideas
• Create MOC (Map of Content) notes that curate references by theme
• Use tags consistently to enable cross-cutting queries
• Link literature notes to project notes where the reference is cited
• Create methodology notes that reference the papers using each method

Dataview Integration

• Use the Dataview plugin to create dynamic literature dashboards
• Query literature notes by tag, date, status, or any frontmatter field
• Generate reading lists filtered by topic and reading status
• Create citation frequency tables showing your most-used references
• Build project-specific reference lists from linked literature notes

Graph View Usage

• The Obsidian graph view shows the link structure between all notes
• Clusters of densely linked literature notes indicate research themes
• Isolated literature notes may need more connections or may be peripheral
• Hub notes (with many connections) are candidates for synthesis writing
• Use the graph to discover unexpected connections between research areas

Multi-Tool Workflows

Zotero to Obsidian Pipeline

• Export from Zotero via Better BibTeX to keep the .bib file continuously updated
• The citation plugin detects changes to the .bib file automatically
• Create literature notes in Obsidian for papers annotated in Zotero
• Use Zotero for PDF management and Obsidian for knowledge synthesis
• This separation leverages the strengths of each tool

Writing Pipeline

• Draft manuscripts in Obsidian using Pandoc-compatible citation syntax
• Use Pandoc to compile Markdown to LaTeX, DOCX, or HTML with formatted citations
• The citation keys in your notes map directly to your bibliography file
• Generate bibliographies automatically from cited references
• This pipeline supports any citation style via CSL

Integration with Research-Claw

This skill enhances the Research-Claw knowledge management workflow:

• Create literature notes programmatically from search results
• Build connected knowledge bases that inform writing and analysis tasks
• Enable citation insertion during AI-assisted manuscript drafting
• Connect with other Obsidian and Zotero skills for comprehensive workflows
• Support systematic review note-taking with structured templates

Best Practices

• Keep your bibliography file in the Obsidian vault for reliable path resolution
• Use a consistent citation key format across all tools in your workflow
• Create literature notes soon after reading to capture fresh insights
• Review and update literature notes periodically as your understanding deepens
• Use templates to ensure consistent structure across all literature notes
• Back up both the bibliography file and the vault regularly