academic-wiki

academic-wiki

A Claude Code plugin (with a bundled MCP server) that builds a persistent, compounding knowledge base of academic papers inside an Obsidian vault. Ingest by arXiv ID, DOI, PDF, or web clipping; the LLM extracts, deduplicates, versions, and synthesizes — papers, concepts, methods, claims, results — into a graph of cross-linked markdown.

It applies Andrej Karpathy's LLM-Wiki pattern (refs/llm-wiki.md), but specialized for academic data: identifiers and dedup, BibTeX export, paper versioning, snapshots for reproducibility.

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How this differs from Karpathy's llm-wiki

Karpathy's llm-wiki is a generic LLM wiki for articles, web clippings, and free-form notes. academic-wiki keeps the same core pattern (raw → wiki → schema, with ingest / compile / query / lint) but adds machinery you need when the sources are scholarly papers:

	llm-wiki (Karpathy)	academic-wiki (this project)
Domain	Generic articles, web pages, notes	Academic papers
Operations	6: init, ingest, compile, query, lint, remove	8: adds export-bibtex, snapshot
Source types	Plain markdown / URL	arXiv ID (with version), DOI, PDF, web clipping, pre-extracted markdown
Identity	Source filename	paper-id (stable, hyphenated) + citation-key (BibTeX) + identifiers (DOI / arXiv / URL)
Deduplication	None	Two-pass: byte-SHA, then identifier match across DOI / arXiv / URL — same paper from different sources collapses to one paper-id
Versioning	None	arXiv v1, v2... resolved to one canonical paper with .versions.yml history
BibTeX	n/a	Per-paper raw/bib/<paper-id>.bib; consolidated export filtered by project / field / tag / keys / natural-language query
Snapshots	Vault-shared git	Each wiki is its own nested git repo; snapshot <label> creates an annotated tag for reproducibility (e.g. conference submission)
Page taxonomy	Concepts, people, sources	Papers + concepts + methods + claims + results + open-problems + authors + venues + queries
Tag scheme	Free-form	Reserved prefixes auto-applied: field/*, subfield/*, method/*, year/*, venue/*; user-controlled: project/*, user/*
Bibliography model	n/a	references-raw (verbatim) → cites (resolved to internal paper-ids) → sources (papers informing a non-paper page)
Conflict policy	Implicit	Explicit: prior text preserved, new evidence appended, contradictions flagged with [!WARNING] callouts — nothing silently overwritten
Bundled tooling	qmd auto-install	qmd auto-install + academic_wiki_mcp server: download_paper, doi_to_bibtex, semantic_scholar_search, get_paper_by_doi, discover_related
Wave structure	n/a	Wave 1 = paper pages only; Wave 2 = entity extraction + cross-paper synthesis (candidate-only, never auto-promoted)

If you're tracking generic web articles and personal notes, use Karpathy's llm-wiki. If your sources are papers and you need stable IDs, BibTeX, and reproducible snapshots, use this.

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Project layout

academic_wiki/
├── .claude-plugin/          # plugin manifest (marketplace.json)
├── commands/wiki.md         # /academic-wiki:wiki slash command
├── skills/wiki/             # the SKILL.md the LLM follows
├── hooks/                   # SessionStart hook (qmd / marp auto-install)
├── scripts/                 # academic_wiki_lib helpers (Python)
├── academic_wiki_mcp/       # bundled MCP server (paper downloads, BibTeX, S2 discovery)
├── tests/                   # pytest suite
├── docs/                    # design specs and plans
└── refs/llm-wiki.md         # Karpathy's original idea

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Prerequisites

• Python 3.10+ — academic_wiki_lib helpers and the MCP server
• git with user.name and user.email configured
• Obsidian vault at ~/Documents/Obsidian Vault/03-Resources/ (note the space in the directory name)
• Node.js 18+ (optional) — auto-installs qmd and marp-cli via the SessionStart hook
• Existing skill ocr-papers-to-latex — used by ingest for local-PDF extraction
• Existing MCP agentic-rag-v2 — used by ingest for arXiv / DOI / publisher fetching (download_arxiv, doi2content, fetch_publisher_html)

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Install — Claude Code plugin

The plugin gives you the /academic-wiki:wiki slash command in Claude Code.

git clone [email protected]:tung491/academic-wiki.git
cd academic-wiki
claude plugin marketplace add .
claude plugin install academic-wiki

Or install directly without registering the marketplace:

claude plugin install ./    # from the cloned repo

Verify in a Claude Code session:

/academic-wiki:wiki

You should see the usage line listing all 8 operations.

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Install — academic_wiki_mcp server