JS PD Knowledge Base

This wiki is the synthesis layer above the canonical by-photo corpus.

The 447 by-photo Markdown files in data/processed/markdown/by-photo/ remain the source of truth. KB pages here make the corpus easier to navigate without summarising away source-level detail. See Build Note for build rules.

Start Here

• Sidebar - hierarchical navigation across the whole KB
• Build Note - what this KB is and how it’s built
• Build Log

Maps

• Document Outline - top-level pipeline outline
• Navigation Path Index - 376 distinct nav_paths grouped
• Evidence Map - pilot-scope evidence trace
• Pilot Source Coverage - GBA-PD pilot section coverage
• Source Catalog - all 447 sources, chronological
• α-Synuclein Source Boundary Map - Tier 1 / Tier 2 / Tier 3 inclusion-and-delegation map for topics/alpha-synuclein

Sections

Eighteen sections cluster all 447 sources by nav_path topology. Each section page lists its sources grouped by nav-path root.

section	sources
GBA-PD, GD, α-Synuclein Pipeline	198
PINK1	46
Complement	42
Biomarkers and Clinical Outcome Measures	27
Mitochondria, Mitophagy, and 31P MRS	19
Molecular Biology, Proteins, Omics	18
PET, Imaging, and Tracer Development	16
Operations, Strategy, Budget, Process	14
GT	11
Clinical PD: Diagnosis, Pipeline, Symptoms	9
Brain Banks, Biobanks, Collaborations	9
Genetics, GWAS, PRS, Pathway Analysis	9
Multiple System Atrophy (MSA)	9
Other Mechanisms (TREM2, TAU, TDP43, etc.)	7
Lysosome and Autophagy	5
LRRK2 Pipeline	4
AGS	2
Microglia and Neuroinflammation Imaging	2

Topic Pages (synthesis)

Topic pages contain narrative synthesis built up from sources. The pilot covers GBA-PD only; new topics are seeded from templates/topic.md and should keep source links next to every claim.

• GBA-PD
• GBA Therapeutics
• GBA-PD Biology (GBA / GD / GBA-PD biology, 36 sources)
• GCase Therapeutic Modalities (PET Imaging GBA / GBA Activator / GBA GT / Substrate-pathway correction, 16 sources)
• Brain Banks, Biobanks, and Postmortem Sample Landscape (MJF / NBB / ICBB / Other Biobanks / Biobanks in Japan / standalone Brain Bank, 12 sources)
• BioOrchestra Biomarker Catalog (catalog/index page over the BioOrchestra _182708–_183115 chain, 74 sources; _183050 excluded as α-synuclein Tier 1)
• Biomarkers (GBA-PD pilot)
• Biomarkers and Clinical Outcome Measures
• PARKN GT
• Complement
• 31P MRS
• Molecular Biology, Proteins, and Omics
• PET, Imaging, and Tracer Development
• PD, Pharmacology, and GT Strategy (whole-section synthesis, 11 sources)
• Clinical PD: Pipeline, Diagnosis, Prodromal, Symptom (whole-section synthesis, 9 sources)
• Genetics, GWAS, PRS, eQTL, and Pathway Analysis (whole-section synthesis, 9 sources)
• Lysosome and Autophagy (whole-section synthesis, 5 sources)
• Multiple System Atrophy (MSA)
• SNCA (Tier 1 only; Tier 2 / Tier 3 delegated to sibling topics per boundary map)
• Pipeline Overview (program map; routes to existing topic / entity pages)

topics/by-nav/ holds 154 generated per-nav-root indexes (one per first-level nav_path value). Use those when you know the exact Word navigation heading; use the section pages above when you want a topic-cluster view.

Entities

• Eliglustat
• Ambroxol
• Venglustat
• PR001
• PARKN GT (PFR-4249-100)
• NLRP3 Inhibitor (Marianthi) (PFR-4231-100)
• TAK-341 (MEDI1341)
• SNCA BTV (HDO) (PFR-4067-100)
• SNCA ASO (WAVE)
• aSyn Propagation Suppressor (aSyn Programs umbrella)

Corpus Layers

layer	path	role
Raw evidence	data/raw/photos/	Local-only source photos. Never staged in git.
Canonical corpus	data/processed/markdown/by-photo/	Direct transcription, one Markdown per photo (447).
Figure assets	data/processed/assets/by-photo/	Only assets embedded from corpus Markdown.
Wiki / KB	data/processed/kb/	This synthesis layer with source links back to the corpus.

KB Rules

• Do not replace the by-photo corpus.
• Keep concrete source links near every claim that matters.
• Prefer small topic pages over one large summary.
• Record uncertainty as uncertainty, especially when the source page has Uncertain Spans.
• Use wiki links ([[…]]) for cross-page navigation and Markdown links for exact evidence files.