| name | research-wiki |
| description | Persistent research knowledge base that accumulates papers, ideas, experiments, claims, and their relationships across the entire research lifecycle. Inspired by Karpathy's LLM Wiki pattern. Use when user says "知识库", "research wiki", "add paper", "wiki query", "查知识库", or wants to build/query a persistent field map. |
| argument-hint | [{"subcommand":"ingest|query|update|lint|stats|init"}] |
| allowed-tools | Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply |
Research Wiki: Persistent Research Knowledge Base
Subcommand: $ARGUMENTS
Overview
The research wiki is a persistent, per-project knowledge base that accumulates structured knowledge across the entire ARIS research lifecycle. Unlike one-off literature surveys that are used and forgotten, the wiki compounds — every paper read, idea tested, experiment run, and review received makes the wiki smarter.
Inspired by Karpathy's LLM Wiki pattern: compile knowledge once, keep it current, don't re-derive on every query.
Core Concepts
Four Entity Types
| Entity | Directory | Node ID format | What it represents |
|---|
| Paper | papers/ | paper:<slug> | A published or preprint research paper |
| Idea | ideas/ | idea:<id> | A research idea (proposed, tested, or failed) |
| Experiment | experiments/ | exp:<id> | A concrete experiment run with results |
| Claim | claims/ | claim:<id> | A testable scientific claim with evidence status |
Typed Relationships (graph/edges.jsonl)
| Edge type | From → To | Meaning |
|---|
extends | paper → paper | Builds on prior work |
contradicts | paper → paper | Disagrees with results/claims |
addresses_gap | paper|idea → gap | Targets a known field gap |
inspired_by | idea → paper | Idea sourced from this paper |
tested_by | idea|claim → exp | Tested in this experiment |
supports | exp → claim|idea | Experiment confirms claim |
invalidates | exp → claim|idea | Experiment disproves claim |
supersedes | paper → paper | Newer work replaces older |
Edges are stored in graph/edges.jsonl only. The ## Connections section on each page is auto-generated from the graph — never hand-edit it.
Wiki Directory Structure
research-wiki/
index.md # categorical index (auto-generated)
log.md # append-only timeline
gap_map.md # field gaps with stable IDs (G1, G2, ...)
query_pack.md # compressed summary for /idea-creator (auto-generated, max 8000 chars)
papers/
<slug>.md # one page per paper
ideas/
<idea_id>.md # one page per idea
experiments/
<exp_id>.md # one page per experiment
claims/
<claim_id>.md # one page per testable claim
graph/
edges.jsonl # materialized current relationship graph
Subcommands
/research-wiki init
Initialize the wiki for the current project:
- Create
research-wiki/ directory structure
- Create empty
index.md, log.md, gap_map.md
- Create empty
graph/edges.jsonl
- Log: "Wiki initialized"
/research-wiki ingest "<paper title>" — arxiv: <id>
Add a paper to the wiki:
- Fetch metadata — use arXiv/DBLP/Semantic Scholar to get full metadata
- Generate slug —
<first_author_last_name><year>_<keyword> (e.g., chen2025_factorized_gap)
- Check dedup — if
paper:<slug> already exists, update instead of creating
- Create page —
papers/<slug>.md with full schema (see below)
- Extract relationships — scan the paper's related work / method for connections to existing wiki pages
- Add edges — append to
graph/edges.jsonl
- Update index — regenerate
index.md
- Update gap_map — if the paper reveals new gaps or addresses existing ones
- Rebuild query_pack — regenerate
query_pack.md
- Log — append to
log.md
Paper page schema:
---
type: paper
node_id: paper:<slug>
title: "<full title>"
authors: ["First A. Author", "Second B. Author"]
year: 2025
venue: arXiv
external_ids:
arxiv: "2501.12345"
doi: null
s2: null
tags: [tag1, tag2]
relevance: core # core | related | peripheral
origin_skill: research-lit
created_at: 2026-04-07T10:12:00Z
updated_at: 2026-04-07T10:12:00Z
---
# One-line thesis
[Single sentence capturing the paper's core contribution]
## Problem / Gap
## Method
## Key Results
## Assumptions
## Limitations / Failure Modes
## Reusable Ingredients
[Techniques, datasets, or insights that could be repurposed]
## Open Questions
## Claims
[Reference claim pages: claim:C1, claim:C2, etc.]
## Connections
[AUTO-GENERATED from graph/edges.jsonl — do not edit manually]
## Relevance to This Project
[Why this paper matters for our specific research direction]
/research-wiki query "<topic>"
Generate query_pack.md — a compressed, context-window-friendly summary:
Fixed budget (max 8000 chars / ~2000 tokens):
| Section | Budget | Content |
|---|
| Project direction | 300 chars | From CLAUDE.md or RESEARCH_BRIEF.md |
| Top 5 gaps | 1200 chars | From gap_map.md, ranked by: unresolved + linked ideas + failed experiments |
| Paper clusters | 1600 chars | 3-5 clusters by tag overlap, 2-3 sentences each |
| Failed ideas | 1400 chars | Always included — highest anti-repetition value |
| Top papers | 1800 chars | 8-12 pages ranked by: linked gaps, linked ideas, centrality, relevance flag |
| Active chains | 900 chars | limitation → opportunity relationship chains |
| Open unknowns | 500 chars | Unresolved questions across the wiki |
Pruning priority (when over budget): low-ranked papers > cluster detail > chain detail. Never prune failed ideas or top gaps first.
Key rule: Read from short fields only (frontmatter, one-line thesis, gap summary, failure note). Do not summarize full page bodies every time.
/research-wiki update <node_id> — <field>: <value>
Update a specific entity:
/research-wiki update paper:chen2025 — relevance: core
/research-wiki update idea:001 — outcome: negative
/research-wiki update claim:C1 — status: invalidated
After any update: rebuild query_pack.md, update log.md.
/research-wiki lint
Health check the wiki:
- Orphan pages — entities with zero edges
- Stale claims — claims with
status: reported older than 14 days
- Contradictions — claims with both
supports and invalidates edges
- Missing connections — papers sharing 2+ tags but no explicit relationship
- Dead ideas —
stage: proposed ideas that were never tested
- Sparse pages — pages with 3+ empty sections
Output a LINT_REPORT.md with suggested fixes.
/research-wiki stats
Quick overview:
📚 Research Wiki Stats
Papers: 28 (12 core, 10 related, 6 peripheral)
Ideas: 7 (2 active, 3 failed, 1 partial, 1 succeeded)
Experiments: 12
Claims: 15 (5 supported, 3 invalidated, 7 reported)
Edges: 64
Gaps: 8 (3 unresolved)
Last updated: 2026-04-07T10:12:00Z
Integration with Existing Workflows
Hook 1: After /research-lit finds papers
# At end of research-lit, after synthesis:
if research-wiki/ exists:
for paper in top_relevant_papers (limit 8-12):
/research-wiki ingest paper
for each gap identified:
add_edge(paper.node_id, gap_id, "addresses_gap")
for each explicit relation to existing wiki paper:
add_edge(paper.node_id, target.node_id, relation_type)
rebuild query_pack
log "research-lit ingested N papers"
Hook 2: /idea-creator reads AND writes wiki
Before ideation:
if research-wiki/query_pack.md exists (and < 7 days old):
prepend query_pack to landscape context
treat failed ideas as banlist
treat top gaps as search seeds
still run fresh literature search for last 3-6 months
After ideation (THIS IS CRITICAL — without it, ideas/ stays empty):
for idea in all_generated_ideas (recommended + killed):
/research-wiki upsert_idea(idea)
for paper_id in idea.based_on:
add_edge(idea.node_id, paper_id, "inspired_by")
for gap_id in idea.target_gaps:
add_edge(idea.node_id, gap_id, "addresses_gap")
rebuild query_pack
log "idea-creator wrote N ideas to wiki"
Hook 3: After /result-to-claim verdict
# Create experiment page
exp_id = upsert_experiment(experiment_data)
# Update each claim's status
for claim_id in resolved_claims:
if verdict == "yes":
set_claim_status(claim_id, "supported")
add_edge(exp_id, claim_id, "supports")
elif verdict == "partial":
set_claim_status(claim_id, "partial")
add_edge(exp_id, claim_id, "supports") # partial
else:
set_claim_status(claim_id, "invalidated")
add_edge(exp_id, claim_id, "invalidates")
# Update idea outcome
update_idea(active_idea_id, outcome=verdict)
# If failed, record WHY for future ideation
if verdict in ("no", "partial"):
update_idea failure_notes with specific metrics and reasons
rebuild query_pack
log "result-to-claim: exp_id updated, verdict=..."
Re-ideation Trigger
After significant wiki updates, suggest re-running /idea-creator:
- ≥5 new papers ingested since last ideation
- ≥3 new failed/partial ideas since last ideation
- New contradiction discovered in the graph
- New gap identified that no existing idea addresses
The system suggests but does not auto-trigger. User decides.
Key Rules
- One source of truth for relationships:
graph/edges.jsonl. Page Connections sections are auto-generated views.
- Canonical node IDs everywhere:
paper:<slug>, idea:<id>, exp:<id>, claim:<id>, gap:<id>. Never use raw titles or inconsistent shorthands.
- Failed ideas are the most valuable memory. Never prune them from query_pack.
- query_pack.md is hard-budgeted at 8000 chars. Deterministic generation, not open-ended summarization.
- Append to log.md for every mutation. The log is the audit trail.
- Reviewer independence applies. When the wiki is read by cross-model review skills, pass file paths only — do not summarize wiki content for the reviewer.
Acknowledgements
Inspired by Karpathy's LLM Wiki — "compile knowledge once, keep it current, don't re-derive on every query."