chem-nlm-helper

name	chem-nlm-helper
description	Bridges paper-mentor with NotebookLM. Creates notebooks, adds PDF/URL sources, runs queries with citation-grounded answers. Used by `paper-mentor` Phase 2 to build a literature library and run the 4-question summary on each paper. Triggers on phrases involving NotebookLM operations + chemistry/materials context.
version	0.1.0

chem-nlm-helper — NotebookLM Helper for Chemistry Papers

What this does

This skill is a thin adapter between paper-mentor and NotebookLM. It handles:

1. Detecting whether NotebookLM CLI / MCP is installed
2. Creating notebooks
3. Adding sources (PDFs, URLs, abstracts)
4. Running structured queries (the 4-question summary)
5. Returning citation-grounded answers

If NotebookLM is not installed, this skill guides the user through install before doing anything else.

---

Pre-flight check

ALWAYS run before any NotebookLM call:

1. Check for MCP tools: look for mcp__notebooklm-mcp__* tools in the available tool list
2. Check for CLI: run which nlm via Bash
3. Decide:

if has_mcp_tools:
    use_mode = "mcp"
elif has_cli:
    use_mode = "cli"
else:
    # NotebookLM not installed
    return install_guidance()

Install guidance (when both missing)

Tell the user:

「我看起來找不到 NotebookLM 工具。Phase 2 文獻陪讀需要它。

你有兩個選擇： A. 跑 bash INSTALL.sh（或 Windows 上 INSTALL.ps1）一鍵裝起來 B. 跳過 NotebookLM，我幫你手動讀 abstract（會慢一點，但可以）

要選哪個？」

If they choose A, point them to:

「在 paper-mentor/ 資料夾下跑 bash tools/install_nlm.sh，會自動裝好 nlm CLI 和 MCP server。完成後跑 nlm login 連 Google 帳號，然後重新進來就可以了。」

If they choose B, fall back to manual mode (skip Steps 2-4 below; do summaries by reading abstracts via WebFetch).

---

Step 1: Create notebook

# MCP mode
mcp__notebooklm-mcp__notebook_create(
    title="[student topic] — literature review",
    description="Auto-generated by paper-mentor for Phase 2"
)
# Returns notebook_id

# CLI mode
nlm notebook create "[student topic] — literature review"

Save the notebook_id for subsequent calls.

---

Step 2: Add sources

For each paper from chem-paper-search results:

Source type	Best	Fallback
Has openAccessPdf URL	Add as url	—
Has Semantic Scholar page only	Add the page URL as url	abstract as text
Has DOI only	Construct DOI URL → add as url	abstract as text
Nothing	Add abstract as text source	—

# MCP mode
mcp__notebooklm-mcp__source_add(
    notebook_id=notebook_id,
    source_type="url",
    url="https://example.com/paper.pdf",
    wait=True
)

# CLI mode
nlm source add --notebook {id} --url {pdf_url}

Batch processing: add all sources before running queries (NotebookLM processing time can be 30s-2min per source).

Size limits:

• PDF >50MB → split or use abstract instead
• Total sources per notebook → ≤50 (NotebookLM limit)

---

Step 3: Run the 4-question summary

For each paper, run a NotebookLM query restricted to that one source. Use these 4 questions (the chieh-ting-lin profile may customize wording):

1. 用什麼方法解什麼問題？(具體技術 + 具體挑戰)
2. 結果改進多少？(要具體數字，PCE / 效率 / 穩定性)
3. 機制解釋夠扎實嗎？(只是現象學描述還是有 cross-characterization?)
4. 跟我們的研究方向是補充 / 競爭 / 啟發？

# MCP mode — exact parameter name varies by MCP server version.
# Try in order: source_ids, source_filter, sources. Inspect the tool schema first
# via ListMcpResourcesTool / look at notebook_query docstring before calling.
mcp__notebooklm-mcp__notebook_query(
    notebook_id=notebook_id,
    query="用什麼方法解什麼問題？...",
    # parameter name to be confirmed at call time:
    source_ids=[paper_source_id]  # or source_filter=, depending on MCP version
)

# CLI mode (canonical)
nlm chat {notebook_id} "用什麼方法解什麼問題？" --sources {source_id}

Important: if you cannot confirm the per-source restriction parameter, fall back to CLI mode (which is well-documented). Per-source restriction is required — without it, queries mix all papers in the notebook and the per-paper summary is meaningless.

Output structure (per paper):

### [Paper title] ([Year])
**Method**: [from Q1, with citations]
**Result (numbers)**: [from Q2]
**Mechanism rigor**: ⭐⭐⭐ (3/5) — [reasoning from Q3]
**Relation**: 補充 / 競爭 / 啟發 — [from Q4, one-line why]

---

Step 4: Cross-paper synthesis (optional)

If user wants a literature map (not just per-paper summaries), run synthesis queries on the WHOLE notebook (not source-restricted):

1. 「這些論文最有共識的發現是什麼？」
2. 「最有爭議或矛盾的點是什麼？」
3. 「哪些方法是重複出現的標配？」
4. 「最近 2 年的趨勢跟更早的有什麼不同？」

This produces the gap report input for paper-mentor Phase 2 Step 5.

---

Step 5: Cleanup (optional)

When done with the project:

# MCP mode
mcp__notebooklm-mcp__notebook_delete(notebook_id=notebook_id, confirm=True)

Don't auto-delete — students may want to come back. Only delete on explicit request.

---

Common issues

Issue	Fix
nlm login failed	Check Google account permissions for NotebookLM. Try again.
PDF processing stuck	Wait up to 2 min, then check nlm source list. If stuck, re-add.
Query returns no citations	Source may have failed processing. Re-check source status.
MCP tool not responding	Restart Claude Code session; MCP server may have died.
Quota exceeded	Free tier of NotebookLM has limits. Upgrade or use less.

---

Hard rules

1. Never run queries without sources — they will hallucinate.
2. Always check wait=True succeeded before querying — querying mid-processing returns garbage.
3. Always pass source_filter for per-paper questions (Step 3) — without it, NotebookLM mixes papers.
4. Quote citations exactly as NotebookLM returns them — do not paraphrase paper titles.
5. If install was skipped, fall back gracefully — don't crash.