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: init|ingest|sync|query|update|lint|stats] 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

Typed Relationships (graph/edges.jsonl)

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. This subcommand is thin wrapping around the canonical helper python3 tools/research_wiki.py ingest_paper …, which is the single implementation of paper ingest in ARIS (per shared-references/integration-contract.md — one helper, no copies). The helper does all of:

1. Fetch metadata — queries the arXiv Atom API when --arxiv-id is given
2. Generate slug — <first_author_last_name><year>_<keyword>
3. Check dedup — skip an existing page unless --update-on-exist
4. Create page — papers/<slug>.md with the schema below
5. Rebuild index.md and query_pack.md
6. Append log.md

Edge extraction (step 5/8 in the old manual flow) is not in ingest_paper; do it as a follow-up with add_edge per relationship identified:

# arXiv-known paper
python3 tools/research_wiki.py ingest_paper research-wiki/ \
    --arxiv-id 2501.12345 --thesis "One-line claim from abstract."

# Venue paper with no arXiv mirror
python3 tools/research_wiki.py ingest_paper research-wiki/ \
    --title "Attention Is All You Need" \
    --authors "Ashish Vaswani, Noam Shazeer, …" --year 2017 --venue "NeurIPS"

# Manual edge after ingest
python3 tools/research_wiki.py add_edge research-wiki/ \
    --from "paper:vaswani2017_attention_all_you" \
    --to "paper:chen2025_factorized_gap" \
    --type "extends" --evidence "Section 3.2: adapts the encoder block …"

Other skills (/research-lit, /arxiv, /alphaxiv, /deepxiv, /semantic-scholar, /exa-search) call the same helper directly in their own last step — they don't re-route through /research-wiki ingest as a subcommand, so they don't need an LLM roundtrip.

/research-wiki sync — arxiv-ids <id1>,<id2>,...

Batch backfill: ingest one or more arXiv IDs that were read earlier without being ingested (e.g., because research-wiki/ was set up after the reading happened, or a hook didn't fire).

# Explicit list
python3 tools/research_wiki.py sync research-wiki/ \
    --arxiv-ids 2310.06770,1706.03762

# From a file (one id per line, # comments ok)
python3 tools/research_wiki.py sync research-wiki/ --from-file ids.txt

Dedup is handled per-id; already-ingested papers are skipped silently. This is the recommended manual repair step (see integration contract §5 Backfill). sync does not scan session traces — callers declare the ids explicitly.

Paper page schema (exactly what ingest_paper emits — do not handwrite alternative fields; lint will flag drift):

---
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"]
added: 2026-04-07T10:12:00Z
---

# <full title>

## 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]

Additionally, when the paper was ingested via --arxiv-id and the arXiv API returned an abstract, the helper appends an ## Abstract (original) section after Relevance to This Project containing the raw abstract text as a blockquote. Manual ingests (no --arxiv-id) do not include this section.

/research-wiki query "<topic>"

Generate query_pack.md — a compressed, context-window-friendly summary:

Fixed budget (max 8000 chars / ~2000 tokens):

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

All paper-reading skills follow the same integration contract (see shared-references/integration-contract.md):

• single predicate — [ -d research-wiki/ ]
• single canonical helper — python3 tools/research_wiki.py ingest_paper …
• concrete artifact — papers/<slug>.md + log.md entry
• backfill — sync --arxiv-ids …
• diagnostic — tools/verify_wiki_coverage.sh

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):
        python3 tools/research_wiki.py ingest_paper research-wiki/ \
            --arxiv-id <id> [--thesis "..."] [--tags "..."]
        for each explicit relation to existing wiki paper:
            python3 tools/research_wiki.py add_edge research-wiki/ \
                --from "paper:<slug>" --to "<target>" \
                --type <extends|contradicts|addresses_gap|...> \
                --evidence "..."
    log "research-lit ingested N papers"

Each paper-reading skill ships its own Step "Update Research Wiki (if active)" that calls the same helper once per paper it touched. The business logic is not duplicated — only the loop over that skill's specific result set differs.

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."