/aris-research-wiki

name: aris-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
license: MIT
metadata:
  author: wanshuiyin/ARIS
  version: "1.0.0"

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](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f): 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 /aris-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

`/aris-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"

`/aris-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]

`/aris-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): lo