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
`7 Experiment Notes/`	lab or empirical work (rename if not relevant)
`8 Meeting Notes/`	supervisor and reading-group notes
`9 Orga/`	templates and Templater commands — 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 also embeds its own local graph inline (Juggl block at the bottom), populated by fetch_references.py.

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.

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.