Encyclopedia Map

Master blueprint for this vault. Build depth before breadth: finish a spine, then expand sideways.

Related: Home

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Target Architecture

flowchart TB
  Home[Home]
  Fund[Fundamentals]
  Hist[History]
  Bact[Bacteriology]
  Vir[Virology]
  Myc[Mycology]
  Par[Parasitology]
  Imm[Immunology]
  Clin[Clinical Micro]
  Lab[Diagnostic Lab]
  Abx[Antimicrobials]
  AMR[AMR]
  BI[Bioinformatics]
  AI[AI in Micro]
  Gloss[Glossary]
  Refs[References]

  Home --> Fund
  Home --> Hist
  Home --> Bact
  Home --> Vir
  Home --> Myc
  Home --> Par
  Home --> Imm
  Home --> Clin
  Home --> Lab
  Home --> Abx
  Home --> AMR
  Home --> BI
  Home --> AI
  Home --> Gloss
  Home --> Refs

  Fund --> Hist
  Fund --> Bact
  Fund --> Lab
  Bact --> Clin
  Lab --> Clin
  Abx --> AMR
  Clin --> AMR
  Lab --> BI
  BI --> AI
  BI --> AMR
  AI --> AMR
  AI --> Abx
  BI --> Vir
  AI --> Imm

What each layer should contain

Layer	Contents
MOC	Overview, subtopics, links to notes, open questions
Concept notes	One idea: definition → mechanism → clinical/research relevance
Organism notes	Taxonomy, virulence, disease, diagnosis, treatment, AMR
Method notes	Principle, steps, performance, clinical use
History notes	Who / when / contribution / why it still matters
Glossary	1–3 sentence definitions + links out
Source notes	Book/paper → extract → link to atomic notes

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Priority Backlog

Phase 0 — Navigation ✅

• Home
• Encyclopedia Map
• Frontmatter on major MOCs
• Jawetz Ch1 core concept stubs created

Phase 1 — Foundations spine ✅

Goal: History → germ theory → cell basics → genetics.

Priority	Note / cluster	Status
P1	MOC - Fundamentals of Microbiology	done
P1	History hub + figures	done
P1	Germ Theory · Koch’s Postulates	done
P1	Cell structure cluster	done
P1	Genetics / HGT cluster	done
P1	Pathogen · Normal Microbiota · Microbial Classification · Infectious Disease	done
P2	Metabolism (respiration/fermentation) deep notes	backlog

Phase 2 — Diagnostic spine ✅ (expanded molecular)

Priority	Note / cluster	Status
P1	MOC - Diagnostic & Lab Methods	done
P1	Gram Stain · Acid-Fast Stain · light microscope · Microscopy	done
P1	Extraction: DNA Extraction · RNA Extraction · Plasmid DNA Extraction · Nucleic Acid Quantification · Sample Types and Specimen Quality	done 2026-08-02
P1	PCR family: PCR · qPCR · Multiplex PCR · Digital PCR · Nested PCR · Broad-Range 16S PCR · RT-PCR	done
P1	New NAAT: Isothermal NAAT · CRISPR-based Diagnostics · Syndromic Molecular Panels	done
P1	Genome wet lab: NGS Library Preparation · Targeted Enrichment · Sanger Sequencing · Whole-Genome Sequencing · Metagenomic NGS	done
P1	Culture and Isolation · Antimicrobial Susceptibility Testing · MALDI-TOF MS	done
P2	Serology / antigen deep notes	backlog

Phase 3 — Bacteriology core ✅ (25 high-yield pathogens)

Priority	Cluster	Status
P1	MOC - Bacteriology classification tree	done
P1	Staphylococcus aureus · Streptococcus pyogenes · Streptococcus pneumoniae	done
P1	Escherichia coli · Klebsiella pneumoniae · Pseudomonas aeruginosa	done
P2	Clostridioides difficile · Mycobacterium tuberculosis · Acinetobacter baumannii · Enterococcus faecium · Salmonella enterica · Neisseria meningitidis	done (2026-08-02)
P3	Listeria monocytogenes · Streptococcus agalactiae · Haemophilus influenzae · Legionella pneumophila · Mycoplasma pneumoniae · Neisseria gonorrhoeae	done (2026-08-02 pass 2)
P4	Chlamydia trachomatis · Helicobacter pylori · Vibrio cholerae · Campylobacter jejuni · Nontuberculous Mycobacteria · Bordetella pertussis · Treponema pallidum	✅ 2026-08-02

Phase 4 — Clinical + antimicrobials + AMR ✅ (hubs)

Priority	MOC	Status
P1	MOC - Clinical Microbiology syndrome scaffold	done
P1	MOC - Diseases by System + 10 system hubs	done
P1	Individual disease notes (14 starter diseases)	done
P1	MOC - Antimicrobials class scaffold	done
P1	MOC - Antimicrobial Resistance (AMR)	done
P2	AMR deep-dives (MRSA · ESBL · Carbapenemases · VRE · AmpC · Colistin Resistance)	✅ 2026-08-02
P2	More diseases (TB, influenza, HSV enceph, GC, PJI…); drug-class notes	backlog

Phase 5 — Other domains

MOC	Status
MOC - Virology	✅ hub + 4 priority viruses (influenza, HIV, SARS-CoV-2, HSV)
MOC - Mycology	scaffold done — organism pages backlog
MOC - Parasitology	scaffold done — life-cycle notes backlog
MOC - Immunology	scaffold done — core concept notes backlog

Phase 6 — Computational layer ✅ (expanded)

Priority	Item	Status
P1	MOC - Bioinformatics in Microbiology (9 sections)	done
P1	MOC - AI in Microbiology (6 sections)	done
P1	Data foundations: Sequencing Technologies · Sequencing Data Formats · Read QC and Preprocessing	done
P1	Genome layer: Genome Assembly · Genome Annotation · Variant Calling in Bacteria · WGS Bioinformatics Pipeline	done
P1	Population layer: Comparative Genomics · Pangenome Analysis · Plasmid and Mobile Element Analysis · MLST and cgMLST	done
P1	Phylogenetics: Phylogenetic Tree Building · Phylodynamics · Viral Genomics and Surveillance	done
P1	Multi-omics: Microbial Transcriptomics · Proteomics and MALDI Bioinformatics · Structural Bioinformatics	done
P1	Community: Metagenomics · 16S Amplicon Analysis · Metagenome-Assembled Genomes · Microbiome Statistics	done
P1	Practice: Reproducible Bioinformatics Workflows · Public Sequence Databases · FAIR Data and Genomic Surveillance	done
P1	AI foundations: Machine Learning Basics for Microbiology · Deep Learning in Microbiology · Model Evaluation in Clinical Microbiology · AI Ethics in Clinical Microbiology	done
P1	AI algorithm atlas: AI Algorithms in Microbiology + supervised/unsupervised/CNN/transformer/GNN/generative/transfer + Feature Representation for Microbial ML	✅ 2026-08-02
P1	AI applications: AI for Antibiotic Discovery · AI for Vaccine Design · AI in Antimicrobial Stewardship · AI for Outbreak Detection · Digital Microscopy and Image AI · Genotype to Phenotype Prediction	done
P1	Frontier: Protein Language Models · Foundation Models and LLMs in Microbiology	done
P1	Study aids: Computational Microbiology Study Path · Bioinformatics and AI Glossary · Genomics Command-Line Cheatsheet · Bioinformatics Toolkit for Microbiology	done
P1	Figures: Figure - Machine Learning Workflow in Microbiology · Figure - Omics Layers in Microbiology · Figure - Sequencing Platform Comparison	done
P1	Advanced bacteriology genetics (2026-08-02): CRISPR, integrons, IS/Tn, ICEs, GIs, QS, TCS, TA, R–M, operons/sigmas, persisters	done
P1	Advanced bacterial bioinformatics: GWAS, recombination-aware trees, ANI/GTDB, assembly QC, long-read/hybrid, prophage, PopPUNK, contamination, clinical WGS pipelines	done
P1	Advanced AI-for-bacteria: DNA LMs, structure confounding, agentic workflows, biofilm/persistence AI, plasmid-host ML	done
P2	MOC - Public Health & Epidemiology (scaffold — concept notes started)	scaffold
P2	Worked datasets / notebooks, deeper Centner extraction	backlog

Phase 7 — Source pipeline (ongoing)

Source	Action
Jawetz Ch1	Atomic notes largely linked — continue extraction
Later Jawetz chapters	One chapter → many notes
Paper - AMR Database M.Centner 2026	Claim-level notes — use with AMR Gene Databases

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Writing Rules (for this vault)

1. One idea per note when possible; MOCs stay thin hubs.
2. Use templates in 05_Templates for new notes.
3. Always link: note → MOC, note → related methods/organisms, source → atomic notes.
4. Prefer English note titles for graph consistency.
5. Status: draft → active → mastered (methods).
6. After reading a source: update source note and create/update 1–3 atomic notes.

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Definition of “complete enough” for a domain

A domain MOC is “Phase-complete” when it has:

• Overview (all major MOCs)
• Key subtopics listed with links
• ≥5 core concept notes linked (Fundamentals, Bacteriology, Diagnostics, AMR)
• ≥3 organism or method notes linked (Bacteriology / Diagnostics)
• Open questions
• Links to related MOCs and at least one source
• Active recall bank per domain (partial — on many notes, not centralized)

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Learning media system

• Hub: Learning Media Hub
• Template: Template - Learning Aids
• Diagrams folder: 04_Figures_and_Media/Diagrams/
• Pattern on notes: ## Learning Aids → diagram + > [!example] + video table

Phase 8 — Infrastructure & quality ✅

Item	Status
Dashboard - Vault Health + Dashboard - Organisms and Diseases (Dataview)	done
Encyclopedia.base — Bases database views	done
Microbiology Map.canvas — visual index	done
.obsidian/snippets/microbiology.css — domain callouts, tag colours	done
Glossary Index + Glossary - Core Microbiology Terms + Glossary - Clinical and AMR Terms	done
Image Sources and Attribution + first 3 images	done
Link audit: 45 unresolved → 0 real (Vault Audit 2026-08-01)	done
AMR / Public Health / lab-method / organism gap notes (21)	done

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Immediate next actions (remaining backlog)

1. Optional bacteria: Shigella, Corynebacterium diphtheriae, Rickettsia, Borrelia, Leptospira.
2. More viruses (VZV, CMV, EBV, HBV/HCV, measles…) under MOC - Virology.
3. Immunology core notes: innate vs adaptive, antibody classes, complement — MOC - Immunology.
4. Candida + Aspergillus; Plasmodium.
5. Metabolism notes under Fundamentals (respiration, fermentation, oxygen classes).
6. Remaining (TBD) organisms in disease notes: N. meningitidis, Listeria, H. influenzae, GBS, Salmonella.
7. Real images from CDC PHIL — wanted list in Image Sources and Attribution.
8. Wire the Zotero connector into the 01_References/ folder; Jawetz Ch2+ extraction.
9. Add Learning Aids blocks to remaining organism/method notes.