Research Vault

title

Read Me

created

2026-03-13 16:48

last-updated

2026-04-21

aliases

Research Vault

This is a highly opinionated Obsidian template vault optimized for academic research and knowledge management with a frictionless workflow for capturing, synthesizing, and reviewing knowledge.

TL;DR: How This Vault Works

Read papers → capture ideas inline with #idea/emerging tags (no friction)
Each Friday → extract tagged ideas into formal idea notes if they're recurring
When ideas stabilize → write atomic permanent notes and link to concepts
Review actively → use Spaced Repetition plugin to study flashcards by topic
Keep reference materials organized → tools, workflows, methods in one searchable layer

The philosophy: minimize friction at capture, batch the synthesis, automate the review.

Vault Philosophy

This vault is organized around a four-layer knowledge pipeline that minimizes friction while maintaining rigor.

[Zotero] ──── source of truth for papers and annotations
    │
    ├─→ [001_Daily Notes] ──── daily capture & reflections
    │   └→ #idea/emerging, #idea/questions tags
    │
    ├─→ [002_Literature Notes] ──── one note per paper, imported from Zotero
    │   └→ #idea/emerging, #idea/questions tags
    │
    ├──────────────┐
    │              │ (weekly extraction ritual)
    │              ▼
    │   [003_Ideas] ──── idea notes promoted from tag patterns
    │   │
    │   ├──→ [004_Permanent Notes] ──── atomic claims, stable status
    │   │   ├──→ [007_Wiki] ──── concept definitions, evergreen
    │   │   └──→ [006_Projects] ──── active research initiatives
    │   │
    │   └──→ [004_Reference] ──── practical knowledge (tools, workflows, methods)
    │
    ▼
[LaTeX / Overleaf] ──── final paper output

Core philosophy:

Capture ideas inline as you read — low friction, no lost thoughts.
Extract formally once a week — batch processing, clear criteria.
Write permanent notes when ideas stabilize — avoid premature formalization.
Keep reference materials lightweight — organized by function, not by type.
Review flashcards actively — spaced repetition for retention.

Core rules:

Zotero owns all PDFs and annotations. Obsidian never stores raw PDFs.
Literature notes are generated, not hand-written. The template does the scaffolding.
Permanent notes are written from memory, not copy-pasted from literature notes.
Projects are commitments. Maximum three active at any time.
Wiki notes are evergreen definitions, not reading notes. They describe concepts, not papers.
The Inbox is a buffer for urgent captures only. Process weekly.

Folder Structure

vault/
├── .obsidian/              ← Obsidian app settings, plugins, themes, hotkeys
├── .pandoc/                ← Pandoc configuration files for markdown conversion
├── .trash/                 ← Obsidian's trash folder (auto-managed)
├── _attachments/           ← All images and exported figures (managed by Obsidian)
├── _templates/             ← Templater templates — see Section 4
├── 000_Inbox/              ← Emergency buffer only. Process weekly.
├── 001_Daily Notes/        ← Daily research journal, auto-created by Templater
├── 002_Literature Notes/   ← One note per paper, imported via Zotero Integration
├── 003_Ideas/              ← Idea notes promoted from inline tags. Ideas in progress.
├── 004_Permanent Notes/    ← Atomic, evergreen claims written in your own words
├── 005_Reference/          ← Lightweight reference materials (tools, workflows, methods)
│   ├── 005_Reference.md    ← Folder note explaining reference layer
│   ├── Tools/              ← Software docs, command refs, keyboard shortcuts
│   ├── Workflows/          ← Step-by-step processes, SOPs, integration guides
│   ├── Strategies/         ← Field guidance, institutional policies, best practices
│   ├── Methods/            ← Research methodology guides and procedural checklists
│   └── Clipper/            ← Web-clipped articles, AI artifacts, misc resources
├── 006_Projects/           ← Active research projects (max 3). Completed → 999_Archive
├── 007_Wiki/               ← Concept definitions and terminology (atomic knowledge units)
├── 008_MOC/                ← Maps of Content — topic navigation and indexes
├── 999_Archive/            ← Completed projects and abandoned ideas
├── .gitignore              ← Git exclusions for PDFs, workspace, cache
├── .git/                   ← Git repository (managed by Obsidian Git)
└── README.md               ← This file

Each folder contains a folder note (same name as the folder) that explains the purpose, rules, and usage of that folder. Open the folder note before creating content in an unfamiliar folder.

Quick Onboarding: Your First Week

Day 1: Open daily note. Note appears automatically. Click the button bar to understand the four core workflows:

📚 Import a paper from Zotero
🟢 Create a permanent note (if you have an atomic claim ready)
💡 Create an idea note (if you have a research hunch)
📖 Create a concept note (if you encountered a term to define)

Days 2–5: Read papers normally. When you have a thought:

In the literature note: add a ## Ideas section, tag with #idea/emerging
In the daily note: jot thoughts in 💡 section, tag with #idea/emerging or #idea/questions

No need to formalize — just tag and move on.

Friday (Week 1): Do the weekly extraction ritual (30 min):

Open 003_Ideas/003_Ideas.md and browse the "All Idea Tags" query
Look for patterns — ideas appearing 3+ times, questions recurring?
If a pattern is strong, press Ctrl+Shift+I to create formal idea note

After that, your muscle memory builds. The system runs on two rhythms:

Daily (10 min): capture + light review
Weekly (30 min): batch extraction + promotion

Installed Plugins & Their Roles

Zotero Plugins

Since Zotero does not allow plugin syncs, they will be manually stored here for cross-device installations. Only one plugin is mandatory, and the rest are for quality of life.

Plugin	Description	Source	File
Attachment Scanner	Plugin designed to scan attachments and add tags to items with no, missing, or duplicate attachments	https://github.com/SciImage/zotero-attachment-scanner.git	[[attachmentscanner@changlab.um.edu.mo.xpi\|xpi file]]
Better BibTex for Zotero	Plugin for Zotero and (in principle) Juris-M that makes it easier to manage bibliographic data, especially for people authoring documents using text-based toolchains (e.g. based on LaTeX / Markdown). Mandatory	https://github.com/retorquere/zotero-better-bibtex.git	[[better-bibtex@iris-advies.com.xpi\|xpi file]]
Linter for Zotero	Plugin for Zotero to format item metadata. Shortcut to set title rich text; set journal abbreviations, university places, and item languages, etc; detect duplicate items.	https://github.com/northword/zotero-format-metadata.git	[[zotero-format-metadata@northword.cn.xpi\|xpi file]]
Pubpeer Plugin for Zotero	Plugin to show if references in Zotero have PubPeer comments	https://github.com/PubPeerFoundation/pubpeer_zotero_plugin.git	[[zotero-pubpeer@pubpeer.com.xpi\|xpi file]]
Zotero OCR	This Zotero plugin adds the functionality to perform an OCR for the PDFs selected in Zotero. It can add a new PDF including the recognized text, a note with the recognized text only, and HTML (hOCR) file(s). Tesseract OCR is used for the text recognition itself.	https://github.com/UB-Mannheim/zotero-ocr.git	[[zotero-ocr@bib.uni-mannheim.de.xpi\|xpi file]]

Core Workflow Plugins

Plugin	Role
Templater	All note creation. Powers every template in `_templates/`. Also runs folder-specific templates automatically.
Dataview	Live queries throughout the vault. Powers MOCs, project dashboards, and the daily cockpit.
QuickAdd	Hotkey-triggered note creation. 5 commands mapped to `Ctrl+Shift+[W/I/N/M/P]` — see Hotkeys section.
Meta Bind (obsidian-meta-bind-plugin)	Button widgets embedded in folder notes and the daily note. One-click note creation from any context.
Zotero Desktop Connector (obsidian-zotero-desktop-connector)	Imports papers and annotations from Zotero into literature notes.
Obsidian Git	Auto-commits and pushes vault to Gitea every 30 minutes.
Linter	Auto-formats notes on save. Keeps `last-updated` frontmatter field current on every edit.
Spaced Repetition (obsidian-spaced-repetition)	Active recall review using SM2 algorithm. Creates sub-decks by tag (`flashcards/concepts`, etc).

Navigation & Retrieval Plugins

Plugin	Role
Omnisearch	Full-text search including note body, not just filenames. Use `Ctrl+Shift+O`.
Strange New Worlds (obsidian42-strange-new-worlds)	Shows inline backlink counts next to every wikilink. Tells you how connected a note is without opening it.
Tag Wrangler (tag-wrangler)	Rename and merge tags vault-wide. Use when refining the `topic/` and `idea/` taxonomy.
Tag Folder (obsidian-tagfolder)	Visual tag browser in the left sidebar. Navigate the `topic/` hierarchy.
Folder Notes (folder-notes)	Makes folder names clickable — opens the folder note for that folder.
Waypoint (waypoint)	Auto-generates and maintains table of contents inside folder notes.

Note Enhancement Plugins

Plugin	Role
Supercharged Links (supercharged-links-obsidian)	Colors and styles wikilinks based on note properties (e.g. `status`, `type`). Configure in Style Settings.
Pretty Properties (pretty-properties)	Improved property panel rendering. Makes frontmatter easier to read and edit.
Colored Tags (colored-tags)	Applies colors to tags in reading view. Matches the `topic/` color scheme.
Various Complements (various-complements)	Autocomplete for wikilinks, tags, and frontmatter values while typing.
Advanced Canvas (advanced-canvas)	Extended Canvas features for project logic maps.

Writing & Editing Plugins

Plugin	Role
LaTeX Suite (obsidian-latex-suite)	LaTeX snippet expansion in math blocks. Used for inline equations in notes.
Table Editor (table-editor-obsidian)	Easy table creation and editing with keyboard shortcuts.
Automatic Table of Contents (automatic-table-of-contents)	Inserts a live TOC in long notes. Use in project dashboards.
Mermaid Tools (mermaid-tools)	Toolbar for inserting and editing Mermaid diagram blocks.
Mermaid Popup (mermaid-popup)	Quick preview popup for Mermaid diagrams while editing.
Note Toolbar (note-toolbar)	Custom toolbar buttons per folder or note type.
Editing Toolbar (editing-toolbar)	Quick formatting toolbar in editor for bold, italic, links, etc.

Tasks & Calendar

Plugin	Role
Tasks (obsidian-tasks-plugin)	Enhanced task management with due dates, recurrence, and filtering. Used for project to-dos and follow-ups.
Full Calendar (full-calendar-remastered)	Calendar view for notes with date properties. Useful for tracking project timelines.

Presentation & Export Plugins

Plugin	Role
Advanced Slides (obsidian-advanced-slides)	Create slideshows from markdown notes for presenting research.
Image Converter (image-converter)	Converts pasted images to WebP/JPEG on import to keep `_attachments/` lean.
Pandoc Extended Markdown (pandoc-extended-markdown)	Extended markdown syntax support for advanced formatting.
Pandoc Reference List (obsidian-pandoc-reference-list)	Auto-generates reference lists from Zotero metadata in markdown.
Style Settings (obsidian-style-settings)	Central configuration panel for theme and plugin visual settings.

Utility Plugins

Plugin	Role
GitHub Link (github-link)	Quickly copy formatted GitHub links with line numbers for code references.
Vertical Timeline List (vertical-timeline-list)	Display notes as a vertical timeline for chronological browsing.

4. Templates

All templates live in _templates/. They use Templater syntax (<% tp. %>) except tpl-literature-note.md which uses Nunjucks syntax ({{ }}) and is rendered by the Zotero Desktop Connector plugin — not Templater.

Template	Creates	Trigger
`tpl-base.md`	Base schema included by other templates	Not used directly
`tpl-concept.md`	Wiki concept / terminology note	`Ctrl+Shift+W`, Meta Bind button in `007_Wiki`, or folder template
`tpl-daily-notes.md`	Daily journal note	Periodic Notes (auto on startup)
`tpl-folder-notes.md`	Folder description note	Manual via Templater
`tpl-idea.md`	Research idea note	`Ctrl+Shift+I`, Meta Bind button in `003_Ideas`, or folder template
`tpl-literature-note.md`	Paper import from Zotero	Zotero Integration: Import (or button in daily note)
`tpl-moc.md`	Map of Content for a topic	`Ctrl+Shift+M`, Meta Bind button in `008_MOC`, or folder template
`tpl-permanent-note.md`	Atomic permanent note	`Ctrl+Shift+N`, Meta Bind button in `004_Permanent Notes`
`tpl-project-overview.md`	Project dashboard (folder note)	`Ctrl+Shift+P` — creates in `006_Projects/` and prompts for details

Creating Notes

Daily note — opens automatically when Obsidian starts. If it doesn't, press Ctrl+P → "Periodic Notes: Open daily note". The daily note includes a button bar at the top for creating all other note types without leaving the day's context.

Literature note — click the 📚 button in the daily note, or press Ctrl+P → "Zotero Integration: Literature Note". A search modal opens over your Zotero library. The note is created at 002_Literature Notes/{{citekey}}.md.

Permanent note — press Ctrl+Shift+N, click the 🟢 button in 004_Permanent Notes, or use the 🟢 button in the daily note. Templater prompts for the claim as a full sentence, then names the file from it. The permanent note includes a ## Flashcards section with reversible cards tagged #flashcards/permanent-notes.

Idea note — press Ctrl+Shift+I, click the 💡 button in 003_Ideas, or use the 💡 button in the daily note. Templater prompts for the one-sentence spark, then names the file idea-[slug].md. The idea note includes a ## Flashcards section with reversible cards tagged #flashcards/ideas.

Concept / Wiki note — press Ctrl+Shift+W, click the 📖 button in 007_Wiki, or use the 📖 button in the daily note. Templater prompts for the term and an optional citekey, then names the file concept-[slug].md and places it in 007_Wiki/. The concept note includes a

Flashcards section with reversible cards tagged `#flashcards/concepts`.

MOC — press Ctrl+Shift+M, click the 🗺️ button in 008_MOC, or use the 🗺️ button in the daily note.

Project — press Ctrl+Shift+P (QuickAdd). Templater prompts for the project name, topic tags, and an originating idea. The command creates the project folder and its folder note under 006_Projects/. The folder note is the project dashboard — there is no separate _overview.md. Set project-id immediately after creation and never change it.

Property Schema

Properties are defined in .obsidian/types.json and committed to Git. All devices share the same property type definitions automatically.

Consistent Properties (all note types)

Property	Type	Purpose
`type`	Text	Note kind — drives vault-wide Dataview filters
`created`	Date	Creation date `YYYY-MM-DD` — set by template
`status`	Text	Processing or pipeline state — values vary by type
`tags`	Tags	Obsidian tag type — always include `type/` and `topic/` tags

`type` Values

Value	Note kind	Folder
`literature-note`	Imported paper	002_Literature Notes
`permanent-note`	Atomic idea	004_Permanent Notes
`idea`	Research hunch	003_Ideas
`project`	Active research project	006_Projects
`moc`	Map of Content	008_MOC
`concept`	Wiki / terminology note	007_Wiki
`daily-note`	Daily journal	001_Daily Notes
`folder-note`	Folder description	Various

`status` Values by Type

Type	Status values
`literature-note`	`unread` → `annotated` → `processed` → `needs-revisit`
`idea`	`seed` → `growing` → `project-ready` → `abandoned`
`project`	`active` → `paused` → `writing` → `complete`
`concept`	`stub` → `developing` → `stable`

Linking Properties

Property	Type	Used in	Purpose
`projects`	List	literature-note, permanent-note, idea	Project IDs — all note types use the list form for multi-project use
`project-id`	Text	project	Stable slug key — set once at creation, never changed
`origin-idea`	Text	project	The `idea-[slug]` that graduated to become this project
`mocs`	Text	literature-note, permanent-note	Link to parent MOC
`sources`	List	permanent-note	Citekeys of supporting literature
`citekey`	Text	literature-note	BBT citekey — stable link to Zotero and `.bib` file
`related-concepts`	List	concept	Links to other Wiki concept notes
`first-encountered`	Text	concept	Citekey where the term first appeared

Rule: All note types use projects (List) — never project (Text, singular). Always link to a project by its project-id value, not its title. Dataview queries on list fields use contains(projects, "project-id").

The Reading-to-Note Pipeline

Main Workflow: Inline Idea Tagging

1. Discover paper (Google Scholar / Semantic Scholar)
        │
        ▼
2. Import to Zotero via browser connector
        │  BBT assigns citekey automatically
        ▼
3. Read on e-Reader (Zotero Android or iOS)
        │  Highlight only — use color semantics below
        ▼
4. Annotate on iPad or laptop (Zotero iOS / Desktop)
        │  Add typed comments: NOTE: / Q: / LINK: prefix
        ▼
5. Import to Obsidian
        │  Ctrl+P → "Zotero Integration: Literature Note"
        │  Creates 002_Literature Notes/{{citekey}}.md
        ▼
6. Write synthesis sections
        │  Summary, Key Contributions, Methodology, Findings
        │  Connections: link to related [[notes]] and [[MOCs]]
        ▼
7. Capture ideas inline (as you read)
        │  Add ## Ideas section in daily note or literature note
        │  Tag emerging thoughts with #idea/emerging
        │  Tag questions with #idea/questions
        │  Free-form, no structure required — minimize friction
        ▼
8. Weekly extraction ritual (Friday)
        │  Open 003_Ideas/003_Ideas.md
        │  Review all #idea/emerging and #idea/questions tags
        │  Criteria for promotion: recurring theme, 3+ sources, won't leave you alone
        │  Create formal idea note if threshold met → idea-[slug].md
        │  Link back to sources
        ▼
9. Idea → Permanent Note (when ready)
        │  Idea note reaches status: stable
        │  Extract one atomic claim → 003_Permanent Notes/
        │  Link back to idea note as evidence
        │  Consider promoting to concept/wiki if term needs defining
        ▼
10. Link to projects and MOCs
        │  Add topic/ tags → appears in MOC Dataview query
        │  Set projects: field if tied to active project
        ▼
11. Git auto-commits (every 30 min)

Highlight color Semantics (Zotero)

Consistent colors make annotation import meaningful.

color	Label	Use for
🟡 Yellow	`Key-Claim`	Main argument, central contribution
🔵 Blue	`Method`	Approach, technique, experimental design
🟢 Green	`Evidence`	Data, results, supporting findings
🔴 Red	`Critique`	Limitation, disagreement, gap
🟣 Purple	`Definition`	Term or concept being defined
🟠 Orange	`Follow-Up`	Needs further reading, unresolved question

These map automatically to Obsidian callout labels via the Nunjucks template.

Annotation Comment Prefixes (typed in Zotero)

NOTE:   your own thought or observation
Q:      question to chase in another paper
LINK:   connection to another paper or idea

These render under the ↳ arrow in the imported literature note callout blocks.

Zotero Integration

Import Format Settings

Name:             Literature Note
Output Path:      002_Literature Notes/{{citekey}}.md
Image Output:     _attachments/{{citekey}}/
Image Base Name:  image
Template File:    _templates/tpl-literature-note.md

Re-importing a Paper

The {% persist %} blocks in tpl-literature-note.md protect your written synthesis sections from being overwritten on re-import. Only the Annotations section updates — and only with annotations added since the last import, stamped with the import date.

Never choose "overwrite" when the plugin asks on re-import. The persist system handles the merge safely.

Zotero Must Be Running

The integration reads Zotero's local SQLite database via port 23119. Zotero must be open on the same machine when you trigger an import. This means literature note imports happen on the laptop or desktop only — not on mobile devices.

Data Explorer

Run Ctrl+P → "Zotero Integration: Data Explorer" while Zotero is open. This shows every variable available to the template for the currently selected Zotero item. Use it to debug template rendering issues.

Daily & Weekly Rhythms

Daily (10–15 min)

Daily note auto-creates on startup via Periodic Notes
Glance at Active Context — shows active projects and papers in progress
Use the button bar at the top to create notes without leaving the daily note
Capture reading observations in 📖 Reading Notes (cite inline with [[citekey]])
Capture emerging ideas in 💡 Ideas & Thinking using #idea/emerging tags
- No structure required — minimal friction, just let thoughts flow
- Tag patterns will emerge naturally over the week
Log questions or unresolved thoughts with #idea/questions tags
Use 🗒️ Scratchpad for diagrams, rough outlines, and structural sketches
Review flashcards (10 min) — open Spaced Repetition plugin, target sub-deck by date

Weekly Extraction Ritual (Friday, 30–40 min)

This is where tagged ideas become formal notes.

Open Ideas dashboard — 003_Ideas/003_Ideas.md
- Review "All Idea Tags" Dataview query to surface #idea/emerging and #idea/questions
- Look for patterns: which ideas appear 3+ times? Which ones won't leave you alone?
Promotion criteria — create formal idea note if:
- Same idea appears in 3+ literature/daily notes (recurring theme)
- Evidence comes from multiple sources
- It will still matter next week
Extract to formal idea note
- Press Ctrl+Shift+I or click 💡 in 003_Ideas
- Name: concise question or claim → generates idea-[slug].md
- Link back to originating tags/sources in "Evidence & Literature So Far"
Process the Inbox — every note in 000_Inbox/ gets promoted, linked, deferred, or deleted. Target: empty Inbox.
Import pending literature notes — any papers annotated in Zotero this week that haven't been imported yet.
Check project pulse — one sentence per active project: where did it move, where is it stuck.
Review idea pipeline — scan 003_Ideas/ folder. Any ideas now at status stable ready to extract permanent notes from?
Check MOC dashboard — open 008_MOC/008_MOC.md. Any topic tags that now warrant a new MOC?
Update Wiki concepts — did any new terms emerge this week worth defining? Press Ctrl+Shift+W to create.
Set next week's focus — three intentions, not a task list.

Reference Materials Layer (005_Reference)

005_Reference/ is the vault's lightweight practical knowledge layer. Use it for tools, workflows, strategies, methods, and web-clipped content that support your research but aren't primary literature or ideas.

Reference vs. Other Layers

Layer	Content	Example
Reference (005)	Practical how-to, documentation	"Zotero keyboard shortcuts", "How to run a git rebase", "University publishing timeline"
Literature (002)	Academic papers and their synthesis	"Smith et al (2020) on absorptive capacity"
Permanent (004)	Atomic claims extracted from literature	"Organizations with high R&D investment have higher absorptive capacity"
Idea (003)	Patterns and hunches worth exploring	"Does absorptive capacity vary by firm age?"

Folder Organization

Tools/ — software documentation, command references, keyboard shortcuts

Zotero keyboard shortcuts
Pandoc command reference
Docker cheat sheet

Workflows/ — step-by-step processes, SOPs, integration guides

"How to set up Zotero + Obsidian integration"
"Git workflow for this project"
"Manuscript submission checklist"

Strategies/ — field-level guidance, institutional policies, best practices

Journal's preference for anonymization
University publishing timeline
Funding landscape overview

Methods/ — research methodology guides, procedural checklists

"Designing a literature review protocol"
"Best practices for thematic analysis"
"How to conduct a pilot study"

Clipper/ — web-clipped articles, AI artifacts, miscellaneous resources

Newsletter issue on innovation
Blog post on digital transformation
AI conversation artifact on research methods

Capture Pathways

From Obsidian Web Clipper: → 005_Reference/Clipper/ automatically, or manually sort to appropriate subfolder

From inline tagging in daily notes: → Tag with #reference/ prefix in daily note → Weekly: move/link to appropriate Reference subfolder

Manual creation: → Ctrl+P → "Create file in folder" → navigate to 005_Reference/[subfolder]/

Reference Note Format

Reference notes are ultra-lightweight:

No synthesis required
No complex frontmatter
Just content + source link
Can be as short as a code snippet or one-liner

Minimal friction = actually used when needed.

Flashcard System (Spaced Repetition)

All concept and idea notes include a ## Flashcards section with reversible flashcards optimized for active recall.

Flashcard Formats Supported

Single-line basic (::):

Q: What is absorptive capacity? :: A: The ability to recognize, assimilate, and apply external knowledge

Reversible (:::):

Absorptive Capacity ::: The ability to recognize, assimilate, and apply external knowledge

(Spaced Repetition automatically creates the reverse card: "The ability to… ::: Absorptive Capacity")

Multi-line (?):

Q: Why does absorptive capacity matter?
?
A: Firms with higher absorptive capacity benefit more from knowledge spillovers and external R&D

Cloze deletion (==):

Organizations with higher ==absorptive capacity== benefit more from external knowledge

Sub-Decks by Tag

The Spaced Repetition plugin auto-organizes by tag:

#flashcards/concepts → all concept definitions
#flashcards/permanent-notes → claims from permanent notes
#flashcards/ideas → idea questions and evidence
#flashcards/literature → key findings from papers

Review by sub-deck based on your weekly focus.

Weekly Flashcard Review

Target: 10–15 minutes daily

Open Spaced Repetition plugin in sidebar
Click the target sub-deck (e.g., flashcards/concepts)
Cards appear in randomized order via SM2 algorithm
Review pace: ~6-8 cards per minute
Mark as "Hard" (shows sooner), "OK" (normal), or "Easy" (shows later)

The SM2 algorithm automatically intervals cards based on difficulty — hard cards surface more often, easy cards less frequently.

MOC Management

How MOCs Stay Current Automatically

MOCs use Dataview queries to surface notes by topic/ tag. You never manually add notes to a MOC. Instead:

Tag any note with topic/your-topic in its frontmatter tags
The MOC's Dataview query picks it up automatically
The MOC stays current without any editing

Creating a New MOC

Create a new MOC when a topic/ tag appears on four or more notes. The folder note in 008_MOC/ surfaces this automatically during weekly review.

Press Ctrl+Shift+M (QuickAdd)
  — or —
Click 🗺️ button in 008_MOC folder note
→ Templater prompts for topic name
→ Saves to 008_MOC/MOC - [Topic Name].md

Linking Notes to a MOC

At note creation time, the template prompts you to link to a MOC. The chosen MOC name is written into the mocs: frontmatter field.

For existing notes, add the MOC's name to the mocs: field directly in the note's properties panel.

MOC File Naming

Always prefix with MOC - in folder 008_MOC/:

008_MOC/MOC - Knowledge Management.md
008_MOC/MOC - Innovation Strategy.md
008_MOC/MOC - Absorptive Capacity.md

This keeps them visually grouped in the file list and findable as a set via Omnisearch.

Wiki / Concept Notes

007_Wiki/ is the vault's terminology layer. A concept note is not a paper summary — it is an evolving definition of a term or construct that appears across multiple papers and projects.

Concept Notes vs. Permanent Notes

	Concept note	Permanent note
Subject	A term or construct	A claim or argument
Form	"What is X?"	"X causes Y because Z"
Example	`concept-absorptive-capacity.md`	`firms-need-prior-knowledge-to-absorb-new-knowledge.md`
Updates	Grows richer over time	Stays atomic; link to it instead of editing

Use a concept note when you encounter a term you want to track across the literature. Use a permanent note when you want to record a specific claim about that term.

Concept Note Lifecycle

stub      ← created on first encounter; just a term + definition
  │
developing ← additional sources, related terms, counter-definitions added
  │
stable    ← settled definition; linked from MOCs and permanent notes

Promote status during weekly review as more sources accumulate.

Creating a Concept Note

Press Ctrl+Shift+W (QuickAdd)
  — or —
Click 📖 button in 007_Wiki folder note
  — or —
Click 📖 button in daily note button bar
→ Templater prompts for term name and optional citekey
→ Saves to 007_Wiki/concept-[slug].md

Linking Concept Notes to MOCs

The MOC template includes a Dataview query that pulls all concept notes tagged with a matching topic/ tag. Tag concept notes with the same topic/ tags you use on literature and permanent notes — they appear in the MOC automatically.

Project Workflow

Starting a Project

Press Ctrl+Shift+P (QuickAdd) — Templater prompts for the project name, then creates 006_Projects/[Project Name]/[Project Name].md
Open the new folder note immediately and set project-id — a lowercase hyphenated slug. This is the stable key; never change it after creation.
Set status: active and a deadline
Optionally set origin-idea to the idea note slug this project grew from

The folder note is the project dashboard — there is no separate _overview.md. All Dataview queries, key sources, and the argument outline live in the folder note.

Linking Notes to a Project

In any literature, permanent, or idea note, set:

projects:
  - your-project-id          ← must match project-id exactly
  - another-project-id       ← all note types support multiple projects

The project dashboard's Dataview queries surface all linked notes automatically via WHERE contains(projects, this.file.name).

Project Limit

Maximum three active projects (status: active or status: writing). If you want a fourth, one of the existing three must move to paused or complete first.

Completing a Project

Change status: complete in the project folder note
Move the entire project folder from 006_Projects/ to 999_Archive/
Do not move the literature or permanent notes — they stay in their folders
The archived project's Dataview queries still work from the Archive

Tagging System

Tags are hierarchical using the / separator. Use Tag Wrangler to rename or merge tags. Use Tag Folder in the sidebar to browse the hierarchy.

Tag Hierarchy

# Note type — always include one
type/literature-note
type/permanent-note
type/idea
type/project
type/moc
type/daily-note
type/weekly-review
type/folder-note

# Idea capture (used inline in daily/literature notes)
# Tag emerging thoughts as you read — extract to formal ideas weekly
idea/emerging           ← nascent thoughts, rough ideas
idea/questions          ← unresolved questions, gaps to explore

# Flashcard organization (auto-created by templates)
flashcards/concepts     ← definition cards for wiki concepts
flashcards/ideas        ← question/evidence cards for idea notes
flashcards/permanent-notes ← claim cards for permanent notes
flashcards/literature   ← key findings from papers

# Reference materials organization
reference/tools         ← software docs, command references
reference/workflows     ← step-by-step processes, SOPs
reference/strategies    ← field guidance, institutional knowledge
reference/methods       ← research methodology guides
reference/clipper       ← web clips, AI artifacts, misc

# Research domain — apply to literature and permanent notes
topic/nlp
topic/transformers
topic/evaluation-metrics
topic/causal-inference
topic/machine-learning

# Methodology
method/qualitative
method/quantitative
method/survey
method/meta-analysis
method/experimental

# Processing flags — mirrors status field for tag-based filtering
status/needs-revisit
status/processing

Rules

Every note gets exactly one type/ tag matching its type: property.
Idea capture: use #idea/emerging and #idea/questions inline in daily and literature notes. No formal structure required — tag as you think.
Every literature and permanent note gets at least one topic/ tag.
method/ tags are optional but useful for methodology-focused MOCs.
flashcards/ tags are auto-added by templates — do not create manually.
Do not create status/ tags for every status value — only needs-revisit is worth tagging since it makes papers retrievable via Tag Folder quickly.

Git & Sync

Obsidian Git Configuration

Backup interval:       30 minutes
Auto pull interval:    30 minutes
Commit message:        vault: {{date}} — {{numFiles}} files
Pull on startup:       enabled
Push on backup:        enabled
Pull before push:      enabled

What Is and Isn't Committed

Committed:

All note content (.md files)
.obsidian/plugins/
.obsidian/themes/
.obsidian/snippets/
.obsidian/types.json       ← property type definitions
.obsidian/app.json         ← core settings
.obsidian/hotkeys.json
.obsidian/community-plugins.json

Not committed (.gitignore):

.obsidian/workspace.json
.obsidian/workspace-mobile.json
.obsidian/cache
_attachments/**/*.pdf
*.pdf
*.epub
.DS_Store
Thumbs.db

Manual Git Operations

Obsidian Git plugin toolbar buttons handle day-to-day operations. For manual control, use the Source Control pane (Ctrl+P → "Obsidian Git: Open Source Control View") or the terminal.

Backup Redundancy

The Gitea repo is the primary backup. For secondary redundancy:

Enable Gitea repo mirroring to push to a second remote (Codeberg or private GitHub)
For the Zotero database separately: add ~/.zotero/ to your system backup rotation

15. Cross-Device Notes

Device	Obsidian	Zotero	Primary use
Linux PC	✅ Full desktop	✅ Full desktop	Note synthesis, literature import, writing
macOS	✅ Full desktop	✅ Full desktop	Same as Linux
iPad	✅ iOS app + Working Copy	✅ iOS app	Typing annotations, reviewing notes, Canvas
Android Tablet	❌ Not used	✅ Android app	Reading and highlighting PDFs only

iPad Git Sync

Obsidian iOS uses Working Copy as the git backend:

Working Copy clones the Gitea repo
Obsidian iOS vault is set to the Working Copy folder
Obsidian Git plugin handles commits and push/pull from inside Obsidian

Commit from the iPad before switching to the desktop to avoid conflicts.

e-Reader (Android Tablet)

The Boox runs Zotero Android only. After a reading session:

Annotations sync to Zotero automatically (requires WiFi)
Open Zotero on the desktop to confirm sync
Open the paper in Zotero desktop, add typed comments
Then trigger the literature note import in Obsidian

LaTeX Handoff

Bibliography Setup (Better BibTeX)

The .bib file is auto-exported by Better BibTeX in Zotero.

Primary export (for direct LaTeX use in VS Code / Overleaf):

Path: ~/research/library.bib
Format: Better BibTeX JSON → BibTeX
Keep updated: enabled

Vault-local export (required for pandoc export from Obsidian notes):

Add a second BBT auto-export targeting .pandoc/library.bib inside the vault root
Same format, same "keep updated" setting
This keeps the bibliography portable across machines and self-contained in git

In any native LaTeX document:

\bibliography{/home/user/research/library.bib}
\cite{vaswani2017attention}   % uses BBT citekey directly

The Two-Link Convention

This is the core rule for pandoc interoperability. Two syntaxes serve different purposes and can coexist:

Syntax	Purpose	Rendered by
`[@vaswani2017attention]`	Citation — appears in reference list	Pandoc citeproc, Pandoc Reference List plugin
`[[vaswani2017attention]]`	Navigation — links to your literature note	Obsidian only (stripped by pandoc filter)

Use [@citekey] anywhere you intend to cite — in permanent notes, project drafts, argument outlines. Use [[citekey]] when you want a clickable link to navigate to your full literature note within Obsidian.

They can appear together: [@vaswani2017attention] [[vaswani2017attention]] — the citation renders the reference, the wikilink provides the Obsidian navigation.

What breaks without this: If you only use [[citekey]] wikilinks, pandoc has no way to identify citations and your reference list will be empty.

Pandoc Export Workflow

Run from the vault root directory:

# Export a single note to LaTeX
pandoc --defaults .pandoc/defaults.yaml 006_Projects/my-project/draft.md -o draft.tex

# Export to PDF directly (requires a LaTeX distribution installed)
pandoc --defaults .pandoc/defaults.yaml 006_Projects/my-project/draft.md -o draft.pdf

# Export to DOCX (for co-authors or journal submission)
pandoc --defaults .pandoc/defaults.yaml 006_Projects/my-project/draft.md -o draft.docx

# Override the CSL style per-invocation (e.g. for a specific journal)
pandoc --defaults .pandoc/defaults.yaml --csl .pandoc/chicago.csl draft.md -o draft.tex

The .pandoc/defaults.yaml file handles:

Bibliography path (.pandoc/library.bib)
Citation processing (--citeproc)
APA style (.pandoc/apa.csl)
Wikilink stripping (.pandoc/filters/wikilinks.lua)

Obsidian → Pandoc → LaTeX: The Full Pipeline

Obsidian (thinking + drafting)
  │  Use [@citekey] for citations in project draft notes
  │  Use [[citekey]] for navigation to literature notes
  │
  ▼
pandoc --defaults .pandoc/defaults.yaml draft.md -o paper.tex
  │  wikilinks.lua strips [[...]] to plain text
  │  citeproc resolves [@citekey] against library.bib
  │  Generates \cite{} calls and \bibliography{} automatically
  │
  ▼
VS Code / Overleaf (final formatting, journal template)
  │  Import the .tex output
  │  Apply journal class, adjust figures, run BibTeX

Writing Notes That Export Cleanly

In project draft notes and argument outlines, write citation-ready prose:

Transformer models fundamentally changed sequence modelling [@vaswani2017attention].
The attention mechanism was later scaled to multilingual settings [@devlin2019bert],
though critiques of positional encoding remain open [@press2021train].

This renders correctly in Obsidian (Pandoc Reference List plugin shows the reference list) and exports correctly via pandoc without any manual citekey conversion.

Dataview Query Rules (separate from LaTeX)

Use file.tags not tags for tag-based WHERE conditions
Use contains(projects, "id") for List fields, = for Text fields
Date fields must be YYYY-MM-DD format for comparisons to work
Folder paths in FROM must be quoted: FROM "002_Literature Notes"
Use length(file.inlinks) to measure how connected a note is

Quick Reference — Hotkeys

Action	Hotkey
Open daily note	`Ctrl+Shift+D`
Create literature note from Zotero	`Ctrl+P` → Zotero Integration (or 📚 in daily note)
Create permanent note	`Ctrl+Shift+N`
Create idea note	`Ctrl+Shift+I`
Create MOC	`Ctrl+Shift+M`
Create concept / Wiki note	`Ctrl+Shift+W`
Create project	`Ctrl+Shift+P`
Full-text search (Omnisearch)	`Ctrl+Shift+O`
Open graph view	`Ctrl+Shift+G`
Git commit and push	`Ctrl+Shift+S`
Command palette	`Ctrl+P`

Name		Name	Last commit message	Last commit date
.obsidian		.obsidian
.pandoc		.pandoc
000_Inbox		000_Inbox
001_Daily Notes		001_Daily Notes
002_Literature Notes		002_Literature Notes
003_Ideas		003_Ideas
004_Permanent Notes		004_Permanent Notes
005_Reference		005_Reference
006_Projects		006_Projects
007_Wiki		007_Wiki
008_MOC		008_MOC
999_Archive		999_Archive
_attachments		_attachments
_templates		_templates
.gitignore		.gitignore
README.md		README.md

Latest commit

History

Folders and files

Repository files navigation

Research Vault

TL;DR: How This Vault Works

Vault Philosophy

Folder Structure

Quick Onboarding: Your First Week

Installed Plugins & Their Roles

Zotero Plugins

Core Workflow Plugins

Navigation & Retrieval Plugins

Note Enhancement Plugins

Writing & Editing Plugins

Tasks & Calendar

Presentation & Export Plugins

Utility Plugins

4. Templates

Creating Notes

Flashcards section with reversible cards tagged #flashcards/concepts.

Property Schema

Consistent Properties (all note types)

type Values

status Values by Type

Linking Properties

The Reading-to-Note Pipeline

Main Workflow: Inline Idea Tagging

Highlight color Semantics (Zotero)

Annotation Comment Prefixes (typed in Zotero)

Zotero Integration

Import Format Settings

Re-importing a Paper

Zotero Must Be Running

Data Explorer

Daily & Weekly Rhythms

Daily (10–15 min)

Weekly Extraction Ritual (Friday, 30–40 min)

Reference Materials Layer (005_Reference)

Reference vs. Other Layers

Folder Organization

Capture Pathways

Reference Note Format

Flashcard System (Spaced Repetition)

Flashcard Formats Supported

Sub-Decks by Tag

Weekly Flashcard Review

MOC Management

How MOCs Stay Current Automatically

Creating a New MOC

Linking Notes to a MOC

MOC File Naming

Wiki / Concept Notes

Concept Notes vs. Permanent Notes

Concept Note Lifecycle

Creating a Concept Note

Linking Concept Notes to MOCs

Project Workflow

Starting a Project

Linking Notes to a Project

Project Limit

Completing a Project

Tagging System

Tag Hierarchy

Rules

Git & Sync

Obsidian Git Configuration

What Is and Isn't Committed

Manual Git Operations

Backup Redundancy

15. Cross-Device Notes

iPad Git Sync

e-Reader (Android Tablet)

LaTeX Handoff

Bibliography Setup (Better BibTeX)

The Two-Link Convention

Pandoc Export Workflow

Obsidian → Pandoc → LaTeX: The Full Pipeline

Writing Notes That Export Cleanly

Dataview Query Rules (separate from LaTeX)

Flashcards section with reversible cards tagged `#flashcards/concepts`.

`type` Values

`status` Values by Type