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, 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.
• 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: zotero — only search Zotero
• /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" — 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, all.
• If not specified: Default to all — search every available source in priority order (semantic-scholar is excluded from all; it 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: all, semantic-scholar              → all + S2 API

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	mcp__semanticscholar__* MCP 已加载，或 fallback 内联 Python	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

Graceful degradation: If no MCP servers are configured, the skill works exactly as before (local PDFs + web search). Zotero and Obsidian are pure additions.

Workflow

Step 0a: Search Zotero Library (if available)

Skip this step entirely if Zotero MCP is not configured.

Try calling a Zotero MCP tool (e.g., search). If it succeeds:

1. Search by topic: Use the Zotero search tool to find papers matching the research topic
2. Read collections: Check if the user has a relevant collection/folder for this topic
3. Extract annotations: For highly relevant papers, pull PDF highlights and notes — these represent what the user found important
4. Export BibTeX: Get citation data for relevant papers (useful for /paper-write later)
5. Compile results: For each relevant Zotero entry, extract:
   • Title, authors, year, venue
   • User's annotations/highlights (if any)
   • Tags the user assigned
   • Which collection it belongs to

📚 Zotero annotations are gold — they show what the user personally highlighted as important, which is far more valuable than generic summaries.

Step 0b: Search Obsidian Vault (if available)

Skip this step entirely if Obsidian MCP is not configured.

Try calling an Obsidian MCP tool (e.g., search). If it succeeds:

1. Search vault: Search for notes related to the research topic
2. Check tags: Look for notes tagged with relevant topics (e.g., #diffusion-models, #paper-review)
3. Read research notes: For relevant notes, extract the user's own summaries and insights
4. Follow links: If notes link to other relevant notes (wikilinks), follow them for additional context
5. Compile results: For each relevant note:
   • Note title and path
   • User's summary/insights
   • Links to other notes (research graph)
   • Any frontmatter metadata (paper URL, status, rating)

📝 Obsidian notes represent the user's processed understanding — more valuable than raw paper content for understanding their perspective.

Step 0c: Scan Local Paper Library

Before searching online, check if the user already has relevant papers locally:

1. Locate library: Check PAPER_LIBRARY paths for PDF files

   Glob: papers/**/*.pdf, literature/**/*.pdf
   

2. De-duplicate against Zotero: If Step 0a found papers, skip any local PDFs already covered by Zotero results (match by filename or title).

3. Filter by relevance: Match filenames and first-page content against the research topic. Skip clearly unrelated papers.

4. Summarize relevant papers: For each relevant local PDF (up to MAX_LOCAL_PAPERS):

   • Read first 3 pages (title, abstract, intro)
   • Extract: title, authors, year, core contribution, relevance to topic
   • Flag papers that are directly related vs tangentially related

5. Build local knowledge base: Compile summaries into a "papers you already have" section. This becomes the starting point — external search fills the gaps.

📚 If no local papers are found, skip to Step 1. If the user has a comprehensive local collection, the external search can be more targeted (focus on what's missing).

Step 1: Search (external)

• Use WebSearch to find recent papers on the topic
• Check arXiv, Semantic Scholar, Google Scholar
• Focus on papers from last 2 years unless studying foundational work
• De-duplicate: Skip papers already found in Zotero, Obsidian, or local library

arXiv API search (always runs, no download by default):

调用 /arxiv skill 搜索（该 skill 优先用 arxiv MCP，MCP 未加载时 fallback 内联 Python）：

/arxiv "QUERY" — max: 10

或直接调用 mcp__arxiv__* 工具（若 arxiv MCP 已加载）。 MCP 未加载时使用内联 Python 直接调用 arXiv API（返回结构化元数据）。 与 WebSearch 结果合并去重。

Semantic Scholar API search (only when semantic-scholar is in sources):

When the user explicitly requests — sources: semantic-scholar：

/semantic-scholar "QUERY" — max: 10 — type: journal

优先用 mcp__semanticscholar__*（已配置 API Key，速率高）； MCP 未加载时 fallback 内联 Python 调用 S2 免费端点。

Why use Semantic Scholar? Many IEEE/ACM journal papers are NOT on arXiv. S2 fills the gap for published venue-only papers with citation counts and venue metadata.

De-duplication between arXiv and S2: Match by arXiv ID (S2 returns externalIds.ArXiv):

• If a paper appears in both: check S2's venue/publicationVenue — if it has been published in a journal/conference (e.g. IEEE TWC, JSAC), use S2's metadata (venue, citationCount, DOI) as the authoritative version, since the published version supersedes the preprint. Keep the arXiv PDF link for download.
• If the S2 match has no venue (still just a preprint indexed by S2): keep the arXiv version as-is.
• S2 results without externalIds.ArXiv are venue-only papers not on arXiv — these are the unique value of this source.

Optional PDF download (only when ARXIV_DOWNLOAD = true):

After ranking, download top N papers via /arxiv "ARXIV_ID — download — dir: papers/". arxiv MCP 已加载时，PDF 自动存入本地缓存目录，无需重复下载。

• Only download top ARXIV_MAX_DOWNLOAD papers by relevance
• Skip papers already in local library
• 1-second delay between downloads (rate limiting)
• Verify each PDF > 10 KB

Step 2: Analyze Each Paper

For each relevant paper (from all sources), extract:

• Problem: What gap does it address?
• Method: Core technical contribution (1-2 sentences)
• Results: Key numbers/claims
• Relevance: How does it relate to our work?
• Source: Where we found it (Zotero/Obsidian/local/web) — helps user know what they already have vs what's new

Step 3: Synthesize

• Group papers by approach/theme
• Identify consensus vs disagreements in the field
• Find gaps that our work could fill
• If Obsidian notes exist, incorporate the user's own insights into the synthesis

Step 4: Output

Present as a structured literature table:

| Paper | Venue | Method | Key Result | Relevance to Us | Source |
|-------|-------|--------|------------|-----------------|--------|

Plus a narrative summary of the landscape (3-5 paragraphs).

If Zotero BibTeX was exported, include a references.bib snippet for direct use in paper writing.

Step 5: Save Results

Default: Always save the literature review to docs/02_literature_research.md (overwrite if exists). This is the standard output path used by downstream skills (idea-discovery, paper-plan).

• Save paper PDFs to literature/ or papers/ (if downloaded)
• Update related work notes in project memory
• If Obsidian is available, optionally create a literature review note in the vault
• If user specifies a custom path (e.g., — save: path/to/file.md), use that instead

Key Rules

• Always include paper citations (authors, year, venue)
• Distinguish between peer-reviewed and preprints
• Be honest about limitations of each paper
• Note if a paper directly competes with or supports our approach
• Never fail because a MCP server is not configured — always fall back gracefully to the next data source
• Zotero/Obsidian tools may have different names depending on how the user configured the MCP server (e.g., mcp__zotero__search or mcp__zotero-mcp__search_items). Try the most common patterns and adapt.