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 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. 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](../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 >