research-lit

Research Literature Review

Research topic: $ARGUMENTS

Constants

• PAPER_LIBRARY — Local directory containing user's paper collection (PDFs). Check these paths in order:
• papers/ in the current project directory
• literature/ in the current project directory
• 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 | $EXA_FETCHER resolves (canonical name exa_search.py, per integration-contract §2); fetcher handles exa-py SDK + API key internally | AI-powered broad web search with content extraction (highlights, text, summaries). Covers blogs, docs, news, companies, and research papers beyond arXiv/S2. Only runs when explicitly requested via — sources: exa or — sources: all, exa | | 8 | Gemini (MCP / CLI) | gemini | mcp__gemini-cli__ask-gemini tool available, or gemini CLI installed | AI-powered broad literature discovery — decomposes topics into sub-problems, aliases, and variants for wider retrieval. Prefers MCP, falls back to CLI. Only runs when explicitly requested via — sources: gemini or — sources: all, gemini | | 9 | OpenAlex | openalex | $OPENALEX_FETCHER resolves (canonical name openalex_fetch.py, per integration-contract §2) and Python requests module importable | Open citation graph with institutional affiliations, funding data, and comprehensive metadata across 250M+ works. Fully open API. Only runs when explicitly requested via — sources: openalex or — sources: all, openalex |

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:
6. Title, authors, year, venue
7. User's annotations/highlights (if any)
8. Tags the user assigned
9. 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