Vault Audit 2026-08-01

Snapshot of a full quality pass over the encyclopedia, what was fixed, and what remains.

Live version of these checks: Dashboard - Vault Health (Dataview, always current)

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Result

Metric	Before	After
Markdown notes	173	200
Unresolved wiki links (excluding templates)	45	0 real
Notes with no type in frontmatter	13	2 (templates only)
Conflicting values for type	5 variants	normalized
Empty MOC files	2	0
Images in vault	0 usable	3
Dataview queries in use	0	15

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What was wrong, and what was done

1. Mis-named links (5 distinct targets)

Links pointed at note titles that never existed.

Broken link	Now points to
History of Medical Microbiology	Medical Microbiology History
Clinical Microbiology Diagnostics	MOC - Clinical Microbiology
Polymerase Chain Reaction (PCR)	PCR
Book Chapter - Jawetz Ch01 - The Science of Microbiology	Jawetz, Melnick & Adelberg’s Medical Microbiology - Chapter 1
01_References/Books, 01_References/Papers, 04_Figures_and_Media/Timeline	real notes instead of folder paths

2. Two empty MOC files

MOC - Genomics & Bioinformatics and MOC - Microbiology were zero-byte files that older notes still linked to. Both are now redirect stubs pointing at the canonical hubs, so no link breaks and no duplicate hub competes with MOC - Bioinformatics in Microbiology.

3. Broken YAML in lab notes

Gram Stain and light microscope had keys written as "method-name:": — a colon inside the key name. That is legal YAML but creates a property literally called method-name:, so the notes were invisible to every query. Fixed, and type: lab-method added to all nine lab notes.

4. Frontmatter type normalized

figure-note, figure-notes, and figure all existed; now all figures use figure. This is what makes the Figures card view in Encyclopedia.base work.

5. Twenty-one missing notes created

Every remaining unresolved link was a note that should exist. Created:

• AMR: Antimicrobial Resistance · Mechanisms of Antibiotic Resistance · Antibiotics · Antimicrobial Stewardship · Efflux Pumps · ESKAPE Pathogens
• Public health: Epidemiology · Vaccination · Infection Prevention and Control · One Health
• Fundamentals: Human Microbiome · Antigenic Variation · Gene Expression
• Organisms: Mycobacterium tuberculosis · Clostridioides difficile · Acinetobacter baumannii
• Lab: Microscopy · MALDI-TOF MS · Disk Diffusion · Broth Microdilution · MIC Testing

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New infrastructure

Thing	File	Purpose
Health dashboard	Dashboard - Vault Health	Orphans, stubs, missing frontmatter — always current
Content dashboard	Dashboard - Organisms and Diseases	Live tables from note properties
Database views	Encyclopedia.base	Bases: organisms, diseases, MOCs, figures, needs-attention
Visual index	Microbiology Map.canvas	The whole vault as one canvas
Styling	.obsidian/snippets/microbiology.css	Domain callouts, tag colours, diagram framing
Glossary layer	Glossary Index + 2 new glossaries	Definitions separated from concept notes
Image policy	Image Sources and Attribution	Where real images come from; AI-image rule

New callouts available

The CSS snippet adds these — type them like any callout:

> [!clinical] Clinical pearl
> 
> [!lab] At the bench
> 
> [!amr] Resistance angle
> 
> [!compute] Computational note
> 
> [!exam] High-yield
> 
> [!caution-med] Safety
> 
> [!history] Historical note
> 

Enable once in Settings → Appearance → CSS snippets → microbiology (already switched on in appearance.json).

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Remaining backlog, in priority order

1. Domain scaffolds still empty of content — MOC - Virology, MOC - Mycology, MOC - Parasitology, MOC - Immunology have hubs but almost no notes. Highest-value next block: influenza, HIV, SARS-CoV-2, HSV; Candida, Aspergillus; Plasmodium; innate vs adaptive immunity.
2. Mechanism notes — ESBL, MRSA, carbapenemases each deserve their own note rather than table rows.
3. Real images — the wanted list in Image Sources and Attribution (Gram stain, agar plates, disk diffusion, biofilm SEM).
4. Metabolism under Fundamentals — respiration, fermentation, oxygen classes.
5. (TBD) placeholders inside disease notes — mostly organisms not yet written (N. meningitidis, Listeria, H. influenzae, GBS).
6. Zotero pipeline — the connector is installed but unused; wiring it would make the 01_References/ folder self-populating.
7. Active recall system — questions exist on most notes but are not collected or scheduled.

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How to keep it clean

1. Open Dashboard - Vault Health weekly. Sections 3 and 5 should read zero.
2. New note = copy a template, set type and status, link it from a MOC in the same session.
3. Re-run the link audit occasionally:

# from the vault root
$files = Get-ChildItem -Recurse -Filter *.md
$names = @{}; $files | ForEach-Object { $names[$_.BaseName] = $true }
$files | ForEach-Object {
  $t = Get-Content $_.FullName -Raw
  [regex]::Matches($t, '\[\[([^\]\|#]+)') | ForEach-Object {
    $l = $_.Groups[1].Value.Trim()
    if (-not $names.ContainsKey($l)) { "$($l)" }
  }
} | Group-Object | Sort-Object Count -Descending

Related

• Encyclopedia Map · Home · Dashboard - Vault Health