wanshuiyin/research-wiki

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 theorem/headline with an honest PROOF status — born via /proof-checker (see Hook 4) |

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.

Capture and injection hygiene

Before persisting an idea, claim, or experiment note, screen operational noise per capture-antipatterns.md. Resolve the repo from the Codex manifest, then the helper:

if [ -z "${ARIS_REPO:-}" ] && [ -f .aris/installed-skills-codex.txt ]; then
  ARIS_REPO=$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null) || true
fi
CAPTURE_FILTER=""
[ -n "${ARIS_REPO:-}" ] && [ -f "$ARIS_REPO/tools/capture_filter.py" ] && CAPTURE_FILTER="$ARIS_REPO/tools/capture_filter.py"
[ -z "$CAPTURE_FILTER" ] && [ -f tools/capture_filter.py ] && CAPTURE_FILTER="tools/capture_filter.py"

Run python3 "$CAPTURE_FILTER" - on the note when resolved. If it flags an environment failure, transient error, or negative tool-capability claim, store the fix/config/workaround instead, or drop the note. Warn-and-skip if the helper is unresolved. research_wiki.py itself quarantines prompt-injection patterns in graph evidence and query-pack rebuilds per injection-hygiene.md; never bypass that writer with freehand graph edits.

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 "$ARIS_REPO/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:

ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null)}"
WIKI_SCRIPT=""
[ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
[ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
[ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"

# arXiv-known paper
[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
    --arxiv-id 2501.12345 --thesis "One-line claim from abstract."

# Venue paper with no arXiv mirror
[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
    --title "Attention Is All You Need" \
    --authors "Ashish Vaswani, Noam Shazeer, …" --year 2017 --venue "NeurIPS"

# Manual edge after ingest
[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" 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
[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" sync research-wiki/ \
    --arxiv-ids 2310.06770,1706.03762

# From a file (one id per line, # comments ok)
[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" 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):

| Section | Budget | Content | |---------|--------|---------| | Project direction | 300 chars | From AGENTS.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: refuted

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 still status: drafted or status: unproven 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 (8 verified, 4 unproven, 2 refuted, 1 sound-modulo-imports)
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 "$ARIS_REPO/tools/research_wiki.py" ingest_paper …
• concrete artifact — papers/<slug>.md + log.md entry
• backfill — sync --arxiv-ids …
• diagnostic — verify_wiki_coverage.sh (Policy E; resolved per integration-contract §2)

Hook 1: After /research-lit finds papers

# At end of research-lit, after synthesis:
if research-wiki/ exists:
    ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null)}"
    WIKI_SCRIPT=""
    [ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
    [ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
    [ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"
    for paper in top_relevant_papers (limit 8-12):
        [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
            --arxiv-id <id> [--thesis "..."] [--tags "..."]
        for each explicit relation to existing wiki paper:
            [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" 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 (CRITICAL — runs on EVERY generation, incl. a re-run with updated constraints): the page write is the deterministic upsert_idea helper, not freehand.

for idea in all_generated_ideas (recommended + killed):
    python3 "$WIKI_SCRIPT" upsert_idea research-wiki/ --slug <stable-id> --title <title> \
         --stage <proposed|archived> --outcome pending --thesis <...> --risks <...> \
         --based-on <paper:slug,...> --target-gaps <G2,...>
    # one call: writes ideas/<slug>.md, wires inspired_by/addresses_gap edges, rebuilds
    # index + query_pack, logs. Default skip-on-exist (won't clobber an idea enriched
    # by /result-to-claim). `outcome` ∈ {unknown,pending,negative,mixed,positive} — the
    # experiment verdict is set later by /result-to-claim, never guessed at ideation.
log "idea-creator wrote N ideas to wiki"

Hook 3: After /result-to-claim verdict

# Create/refresh the experiment node FIRST via add_experiment (verdict owner →
# --update-on-exist). add_edge does NOT verify node existence, so gate the
# supports/invalidates edges on the node having been born (EXP_NODE_OK).
EXP_NODE_OK = (python3 "$WIKI_SCRIPT" add_experiment research-wiki/ --slug <exp_id> \
  --idea idea:<active_idea> --verdict <yes|partial|no> --confidence <high|medium|low> \
  --metrics <...> --reasoning <...> --provenance <run dir> --update-on-exist) succeeded

# Record empirical support as EDGES ONLY, and ONLY if EXP_NODE_OK — never set a claim's
# `status`. A claim's `status` is the PROOF axis (verified / sound-modulo-imports /
# refuted / unproven / drafted / retracted), owned by /proof-checker (Hook 4). The ARIS
# helper REJECTS "supported"/"partial"/"invalidated" as claim statuses.
if EXP_NODE_OK:
    for claim_id in resolved_claims:
        if verdict == "yes":
            add_edge(exp_id, claim_id, "supports")
        elif verdict == "partial":
            add_edge(exp_id, claim_id, "supports")  # partial — qualify in evidence
        else:
            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=..."

Hook 4: Claim birth — from /proof-checker (the ONLY birth point)

Wiki claim nodes are born here. /proof-checker mints a claim node for each top-level theorem/headline after writing PROOF_AUDIT.json, stamping an honest PROOF-axis status and a provenance pointer. No other skill creates a claim node: /result-to-claim (Hook 3) only adds empirical supports/invalidates edges to an already-born claim and never edits its status.

python3 "$WIKI_SCRIPT" add_claim research-wiki/ --slug thm-main-ub \
     --name "Main upper bound" --status verified \
     --provenance "<proof-checker trace dir>" --statement "..." --update-on-exist

Claim status ∈ {drafted, unproven, sound-modulo-imports, verified, refuted, retracted} — the proof axis only. Empirical support is a separate axis carried by edges (Hook 3), never written into status.

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 context isolation applies. When the wiki is read by reviewer skills, pass file paths only; base Codex review is same-family provisional.

Acknowledgements

Inspired by Karpathy's LLM Wiki — "compile knowledge once, keep it current, don't re-derive on every query."