personal-knowledge

name	personal-knowledge
description	Personal Knowledge Management - Integrates 44 papers, 33 literature reviews, 90+ project outputs into structured searchable knowledge. Converts scattered step_*.md, reference_*.md, paper.tex files into a connected knowledge graph.
version	1.0.0
author	Synthos
license	MIT
allowed-tools	shell (bash, find, grep, awk, sort, uniq), Read (view), Write (write), glob, Edit (edit)
metadata	{"synthos":{"priority":"P1","atom_type":"cognitive_atom","description":"Personal knowledge management - integrates and indexes all research outputs into a structured, searchable knowledge graph","signature":"query: str, scope: str -> knowledge_items: list[dict], gaps: list[str]","related_skills":["knowledge-acquisition","knowledge-extraction","association-discovery","argument-expression","evolution"]}}

Personal Knowledge Management (个人知识管理)

Core Positioning

格物致知，知止而后有定. Collect is not the goal; organization is. 947 reference files and 934 step files are not clutter - they are an unindexed goldmine.

Goal: Convert all Synthos outputs across 98 evolution cycles, 103 paper projects, and 44 formal papers into structured personal knowledge for fast retrieval, cross-connection, and trend analysis.

IO_CONTRACT

• input: query: str - Natural language search query
• input: scope: str = "all" - Search scope (papers/references/output/logs)
• output: knowledge_items: list[dict] - Structured knowledge entries (title, summary, source, date, links)
• output: summary: str - Synthesized answer to the query
• output: gaps: list[str] - Knowledge gaps (valuable but uncovered areas)

Knowledge Domains Index

Domain	Papers	Primary Methods	Keywords
Vestibular (VOR)	15+	ODE, PINN	VOR, saccade, vestibular, compensation, adaptation
Eye Movement	10+	ODE, PINN	saccade, pursuit, fixation, blink, vergence
Inner Ear/Vestibular Disease	8+	ODE, PINN	BPPV, Meniere, vestibular schwannoma, tinnitus
Cornea/Anterior Segment	5+	ODE, PINN	cornea, IOP, sclera, hydration, wound healing
Iris/Sclera	4+	3D modeling, segmentation	iris, sclera, 3D, normalization
Visual-Vestibular Cross	3+	ODE, PINN	auditory-vestibular, tinnitus, multisensory
Breast Cancer Dx	1+	Methodology paper	breast cancer, HCS-3WT, ML
Methodology	7+	Lit review, CRISP-DM	research methods, experimental design, data science
Neurology	4+	Review, case study	PD, concussion, stroke, neurology

Execution Steps

Step 1: Knowledge Scan

Scan all output files:

• Paper files: find outputs/papers -name "*.tex"
• Step files: find . -name "step_*.md"
• Reference files: find . -name "reference.md" -o -name "*-review.md"
• Logs: evolution-log.md, agent-log.md

Step 2: Structure Extraction

Extract from each file:

• Title (from filename, content, or LaTeX title)
• Domain (topic keywords: VOR, PINN, ODE, BPPV, iris, etc.)
• Method (ODE, PINN, literature review, systematic review)
• Date (extracted from filename or content)
• Status (draft/complete/pending/publication)
• Connections (cites other papers, cited by others)

Step 3: Association Building

• Topic networks: papers on same topic
• Method evolution: method progression (e.g., ODE -> PINN)
• Timeline: chronological knowledge progression
• Citation chains: inter-paper citation relationships

Step 4: Knowledge Graph

Generate knowledge-graph.json with:

• Nodes: each knowledge entry
• Edges: topic, method, citation associations
• Properties: date, status, quality score

Step 5: Query Interface

Support these query patterns:

• Domain search: "all papers about VOR"
• Method search: "all studies using PINN"
• Time search: "all outputs from May 2026"
• Status search: "all pending submissions"
• Association search: "which studies use same math methods?"
• Gap discovery: "which areas remain unstudied?"

Quality Control

• P0 Evidence traceability: Every knowledge entry must have a source file
• P1 Atomic reproducibility: Every knowledge extraction step independently executable
• P2 Stability sinking: Validated patterns sink to standard classifications
• P3 Human-machine layering: User decides what knowledge to keep

Output Files

• knowledge-graph.json - Structured knowledge graph
• knowledge-index.md - Knowledge index by topic/time/method
• research-timeline.md - Chronological research progress
• knowledge-roi.md - Time/output ROI analysis per domain

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格物致知，知止而后有定. Scattered knowledge, once organized, becomes wisdom.