research-wiki

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:

1. Create research-wiki/ directory structure
2. Create empty index.md, log.md, gap_map.md
3. Create empty graph/edges.jsonl
4. Log: "Wiki initialized"

/research-wiki ingest "<paper title>" — arxiv: <id>

Add a paper to the wiki:

1. Fetch metadata — use arXiv/DBLP/Semantic Scholar to get full metadata
2. Generate slug — <first_author_last_name><year>_<keyword> (e.g., chen2025_factorized_gap)
3. Check dedup — if paper:<slug> already exists, update instead of creating
4. Create page — papers/<slug>.md with full schema (see below)
5. Extract relationships — scan the paper's related work / method for connections to existing wiki pages
6. Add edges — append to graph/edges.jsonl
7. Update index — regenerate index.md
8. Update gap_map — if the paper reveals new gaps or addresses existing ones
9. Rebuild query_pack — regenerate query_pack.md
10. 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:

1. Orphan pages — entities with zero edges
2. Stale claims — claims with status: reported older than 14 days
3. Contradictions — claims with both supports and invalidates edges
4. Missing connections — papers sharing 2+ tags but no explicit relationship
5. Dead ideas — stage: proposed ideas that were never tested
6. 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."