research-lit

What this skill does

# 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` | `$EXA_FETCHER` resolves (canonical name `exa_search.py`, per integration-contract §2); fetcher handles `exa-py` SDK + API key internally | AI-powered broad web search with content extraction (highlights, text, summaries). Covers blogs, docs, news, companies, and research papers beyond arXiv/S2. **Only runs when explicitly requested** via `— sources: exa` or `— sources: all, exa` |
| 8 | **Gemini** (MCP / CLI) | `gemini` | `mcp__gemini-cli__ask-gemini` tool available, or `gemini` CLI installed | AI-powered broad literature discovery — decomposes topics into sub-problems, aliases, and variants for wider retrieval. Prefers MCP, falls back to CLI. **Only runs when explicitly requested** via `— sources: gemini` or `— sources: all, gemini` |
| 9 | **OpenAlex** | `openalex` | `$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:
   - 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., searc