/research-lit

name: research-lit
description: Search and analyze research papers, find related work, summarize key ideas. Use when user says "find papers", "related work", "literature review", "what does this paper say", or needs to understand academic papers.
argument-hint: "[paper-topic-or-url]"
allowed-tools: Bash(*), Read, Glob, Grep, WebSearch, WebFetch, Write, Agent(aris-fanout-leaf), mcp__zotero__*, mcp__obsidian-vault__*

Research Literature Review

Research topic: $ARGUMENTS

Constants

• **PAPER_LIBRARY** — Local directory containing user's paper collection (PDFs). Check these paths in order:

1. `papers/` in the current project directory 2. `literature/` in the current project directory 3. Custom path specified by user in `CLAUDE.md` under `## Paper Library`

• **MAX_LOCAL_PAPERS = 20** — Maximum number of local PDFs to scan (read first 3 pages each). If more are found, prioritize by filename relevance to the topic.
• **SOURCES = `all`** — Which literature sources to search. Options: `zotero`, `obsidian`, `local`, `web`, `semantic-scholar`, `deepxiv`, `exa`, `gemini`, `openalex`, `all`. Full source table and selection rules: see `## Data Sources` below.
• **ARXIV_DOWNLOAD = false** — When `true`, download top 3-5 most relevant arXiv PDFs to PAPER_LIBRARY after search. When `false` (default), only fetch metadata (title, abstract, authors) via arXiv API — no files are downloaded.
• **ARXIV_MAX_DOWNLOAD = 5** — Maximum number of PDFs to download when `ARXIV_DOWNLOAD = true`.

> 💡 Overrides: > - `/research-lit "topic" — paper library: ~/my_papers/` — custom local PDF path > - `/research-lit "topic" — sources: zotero, local` — only search Zotero + local PDFs > - `/research-lit "topic" — sources: web` — only search the web (skip all local) > - `/research-lit "topic" — sources: web, semantic-scholar` — also search Semantic Scholar for published venue papers (IEEE, ACM, etc.) > - `/research-lit "topic" — sources: all, deepxiv` — use default sources plus DeepXiv > - `/research-lit "topic" — arxiv download: true` — download top relevant arXiv PDFs > - `/research-lit "topic" — arxiv download: true, max download: 10` — download up to 10 PDFs

Data Sources

This skill checks multiple sources **in priority order**. All are optional — if a source is not configured or not requested, skip it silently.

Source Selection

Parse `$ARGUMENTS` for a `— sources:` directive:

• **If `— sources:` is specified**: Only search the listed sources (comma-separated). Valid values: `zotero`, `obsidian`, `local`, `web`, `semantic-scholar`, `deepxiv`, `exa`, `gemini`, `openalex`, `all`.
• **If not specified**: Default to `all` — search every available source in priority order (`semantic-scholar`, `deepxiv`, `exa`, `gemini`, and `openalex` are **excluded** from `all`; they must be explicitly listed).

Examples:

/research-lit "diffusion models"                                    → all (default, no S2)
/research-lit "diffusion models" — sources: all                     → all (default, no S2)
/research-lit "diffusion models" — sources: zotero                  → Zotero only
/research-lit "diffusion models" — sources: zotero, web             → Zotero + web
/research-lit "diffusion models" — sources: local                   → local PDFs only
/research-lit "topic" — sources: obsidian, local, web               → skip Zotero
/research-lit "topic" — sources: web, semantic-scholar              → web + S2 API (IEEE/ACM venue papers)
/research-lit "topic" — sources: deepxiv                            → DeepXiv only
/research-lit "topic" — sources: all, deepxiv                       → default sources + DeepXiv
/research-lit "topic" — sources: all, semantic-scholar              → all + S2 API
/research-lit "topic" — sources: exa                               → Exa only (broad web + content extraction)
/research-lit "topic" — sources: all, exa                          → default sources + Exa web search
/research-lit "topic" — sources: gemini                            → Gemini only (AI-powered broad discovery)
/research-lit "topic" — sources: all, gemini                       → default sources + Gemini discovery
/research-lit "topic" — sources: gemini, semantic-scholar           → Gemini + S2 (broad discovery + venue metadata)
/research-lit "topic" — sources: openalex                          → OpenAlex only (open citation graph + institutions)
/research-lit "topic" — sources: semantic-scholar, openalex         → S2 + OpenAlex (complementary metadata)

Source Table

| Priority | Source | ID | How to detect | What it provides | |----------|--------|----|---------------|-----------------| | 1 | **Zotero** (via MCP) | `zotero` | Try calling any `mcp__zotero__*` tool — if unavailable, skip | Collections, tags, annotations, PDF highlights, BibTeX, semantic search | | 2 | **Obsidian** (via MCP) | `obsidian` | Try calling any `mcp__obsidian-vault__*` tool — if unavailable, skip | Research notes, paper summaries, tagged references, wikilinks | | 3 | **Local PDFs** | `local` | `Glob: papers/**/*.pdf, literature/**/*.pdf` | Raw PDF content (first 3 pages) | | 4 | **Web search** | `web` | Always available (WebSearch) | arXiv, Semantic Scholar, Google Scholar | | 5 | **Semantic Scholar API** | `semantic-scholar` | `$S2_FETCHER` resolves (canonical name `semantic_scholar_fetch.py`, per integration-contract §2) | Published venue papers (IEEE, ACM, Springer) with structured metadata: citation counts, venue info, TLDR. **Only runs when explicitly requested** via `— sources: semantic-scholar` or `— sources: web, semantic-scholar` | | 6 | **DeepXiv CLI** | `deepxiv` | `$DEEPXIV_FETCHER` resolves (canonical name `deepxiv_fetch.py`, per integration-contract §2) **and** `deepxiv` CLI present (`command -v deepxiv`) | Progressive paper retrieval: search, brief, head, section, trending, web search. **Only runs when explicitly requested** via `— sources: deepxiv` or `— sources: all, deepxiv` | | 7 | **Exa Search** | `exa` | `$EX