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:

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):

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."