The vault

The BibFlow vault has a fixed structure. Each folder has one role; the numeric prefixes hold the order in Obsidians file pane.

Folder layout

Folder	Holds
`0 Meta/Library/`	dashboards over your library + Python helpers (auto-refreshed)
`0 Meta/Planning/`	hand-edited project material (Roadmap, supervisor brief)
`1 Literature/`	one note per paper, named by its citekey
`2 Wiki/Concept Notes/`	atomic ideas linked from many papers
`2 Wiki/Method Notes/`	protocols, procedures, recipes
`3 Writing/`	drafts and exported chapters (start sections from the Draft Section Block template)
`7 Experiment Notes/`	lab or empirical work (rename if not relevant)
`8 Meeting Notes/`	supervisor and reading-group notes
`9 Orga/`	templates, Templater commands, and `tp.user` helper scripts — never edited by hand

Navigating with wikilinks

Type [[ anywhere; Obsidian autocompletes from existing notes. [[chuo2020insights]] jumps to that paper note; [[MICP]] jumps to the concept note. The Backlinks pane (right sidebar) shows everything that links back to the open note — instant context.

Graph view

The right sidebars graph icon opens the local graph for the active note: which papers it cites, which concept notes it touches.

The left ribbons graph icon opens the global graph view for the whole vault.

Each literature note ends with a ## Cited works list of the papers it references, populated by Fetch References (fetch_references.py). Every entry is a wikilink, so the note’s local graph and Backlinks pane fill in automatically — and references shared across several papers surface in Shared References.

Search

Shortcut	What it does
Cmd+O	jump to a note by name
Cmd+Shift+F	full-text search across the vault
Cmd+P	command palette (any Obsidian or plugin command)
Option+T	the BibFlow Launcher (Templater commands)

Control notes (the `0 Meta/` folder)

These are dashboards, not content. They auto-populate from your literature notes — open them for a birds-eye view of your library.

Roadmap

Mermaid Gantt chart of your thesis timeline plus a milestone checklist. Built from a single fenced gantt code block — no plugin needed; Obsidian renders Mermaid natively. Edit start dates and durations as the project shifts; chained tasks (after <id>) recalculate automatically.

Best treated as a high-level navigator. For week-by-week task tracking, layer the Tasks plugin on top.

Literature Index

Dataview-rendered list of every note in 1 Literature/ with year, journal, and intext citation. Answers “what have I read on X” without grep.

Literature Index — a Dataview table of all paper notes, sortable by year.

Reading Queue

The same library, grouped by reading status instead of by name. Every paper in 1 Literature/ lands in one of to-read, skimmed, referenced, or fully-read — plus an Unset bucket so newly imported papers never slip through. Set a paper’s status with Set Reading Status (Launcher); the board re-counts on its own. A live answer to “what’s left to read?”.

Paper Metrics

Sortable table of citation counts, FWCI, journal h-index, and open-access status for every paper in your library. Generated by fetch_metrics.py; refresh via Launcher → Refresh Paper Metrics. A fast way to see which papers in your set are most cited in their field.

Paper Metrics — citations, FWCI, journal stats per paper, sorted by impact.

Shared References

Papers cited by 2 or more of your literature notes — i.e. references that keep showing up across your reading. A reliable signal for foundational works you have not read yet. Click any unresolved entry to create that literature note instantly.

Shared References — papers cited by multiple of your notes, with citation counts and source links.

The same shared-references signal is also visible in the global graph view:

Global graph view of the vault. **Green** nodes are papers you have already imported into Obsidian (notes in `1 Literature/`); **grey** nodes are referenced papers you have not yet imported or read. The size of each grey node scales with how many of your imported papers cite it — bigger grey dots are stronger candidates for the next paper to read.

Glossary

Dataview-rendered list of all concept notes in 2 Wiki/Concept Notes/, showing each terms one-line definition.

Glossary — auto-rendered list of concept notes with their definitions.

Each row in the Glossary table is sourced from one concept note in 2 Wiki/Concept Notes/. A concept note looks like this:

A concept note in `2 Wiki/Concept Notes/`. The frontmatter holds the term + definition that the Glossary pulls; the body is yours, with backlinks to the literature notes that mention this concept.

Paper Search (experimental)

OpenAlex-backed keyword search. Define keyword and filter blocks in this notes ## Section headers; run Launcher → Paper Search; ranked results land between auto-generated markers under each section. See Templater commands for caveats and limitations.