academic-chapter-writer

What this skill does

# Academic Chapter Writer

Transform topics into publishable textbook chapters with comprehensive research, proper citations, and human-sounding academic prose.

## Overview

This skill creates full-length academic textbook chapters (5,000-15,000 words) through an agentic workflow:

1. **Research** - Search PubMed, compile 20-30 key references
2. **Plan** - Generate detailed TOC with word counts → GET APPROVAL
3. **Write** - Section-by-section with citations
4. **Compile** - Full chapter with Vancouver-style reference list

## Workflow

### Phase 1: Topic Analysis & Research

When user provides topic:

1. **Clarify scope:**
   - Topic: [exact topic]
   - Level: undergraduate | graduate | professional | advanced
   - Target length: [default 8,000 words]
   - Special focus: [any specific angles]

2. **Research via PubMed MCP:**
   ```
   Use PubMed:search_articles for:
   - Main topic + "review" (find reviews)
   - Main topic + "clinical trial" (find trials)
   - Main topic + "guideline" (find guidelines)
   - Main topic + "meta-analysis" (find syntheses)
   ```

3. **Compile reference library:**
   - Target 20-30 papers
   - Prioritize: NEJM, JAMA, Lancet, JACC, Circulation, EHJ
   - Include: 3-5 landmark trials, 2-3 meta-analyses, 1-2 guidelines, reviews

4. **Report to user:**
   "I've searched PubMed and compiled [N] key references including:
   - [X] landmark trials
   - [X] meta-analyses
   - [X] guidelines/reviews
   
   Ready to generate table of contents?"

### Phase 2: Table of Contents Generation

Generate structured TOC with word allocations:

```markdown
# [Chapter Title]

## 1. Introduction (~500 words)
   - Opening hook (clinical scenario)
   - Scope and importance
   - Chapter overview

## 2. [Historical Context / Background] (~800 words)
   - Evolution of understanding
   - Key milestones
   - Current landscape

## 3. [Core Topic Area 1] (~1,500 words)
   ### 3.1 [Subtopic A]
   ### 3.2 [Subtopic B]
   ### 3.3 [Subtopic C]

## 4. [Core Topic Area 2] (~1,500 words)
   ### 4.1 [Subtopic A]
   ### 4.2 [Subtopic B]

## 5. [Evidence Review / Clinical Data] (~2,000 words)
   ### 5.1 Landmark Trials
   ### 5.2 Meta-analyses
   ### 5.3 Real-world Data

## 6. [Practical Applications / Clinical Pearls] (~1,000 words)
   ### 6.1 [Application A]
   ### 6.2 [Application B]

## 7. [Controversies / Ongoing Debates] (~500 words)

## 8. Future Directions (~400 words)

## 9. Conclusions (~300 words)
   - Key takeaways
   - Practice implications

## References
```

**CRITICAL: WAIT FOR USER APPROVAL**

Present TOC and ask:
"Here's the proposed structure totaling ~[X] words. Please review and:
- [Approve] to proceed with writing
- [Modify] specific sections
- [Regenerate] for different approach"

### Phase 3: Section Writing

After TOC approval, write each section following this pattern:

#### Writing Protocol Per Section

1. **Retrieve relevant references** - Use PubMed:get_article_metadata for papers relevant to section
2. **Apply authentic-voice** - Follow `references/writing-style.md` strictly
3. **Include citations** - Number sequentially [1], [2], etc.
4. **Match target word count** - Within ±10%
5. **Present for review** - After each major section

#### Section Template

```markdown
## [Section Title]

[Opening sentence that grounds reader - specific, concrete, not abstract claims]

[Body paragraphs with citations. Each major claim cited. Mix of sentence lengths. No AI tells.]

[Transition to next section or closing thought]

**Citations used in this section:** [1] Author et al., Journal Year; [2] ...
```

#### Citation Format (Vancouver)

In-text: Sequential numbers [1], [2], [1,3], [4-6]

Reference list format:
```
1. Author AA, Author BB, Author CC. Title of article. Journal Abbrev. Year;Volume(Issue):Pages. doi:xxx
```

### Phase 4: Compilation

After all sections approved:

1. **Merge sections** - Ensure smooth transitions
2. **Number citations** - Sequential through entire chapter
3. **Generate reference list** - Vancouver format, numbered
4. **Format check:**
   - All citation numbers present in reference list
   - Consistent heading styles
   - No orphaned references
   - Word count summary

5. **Present final chapter:**
   ```
   # [Chapter Title]
   
   [Full content with numbered citations]
   
   ## References
   
   1. [Reference 1]
   2. [Reference 2]
   ...
   
   ---
   Total words: X,XXX
   Total references: XX
   ```

## Writing Style (Critical)

### Eric Topol Voice Principles

1. **Evidence-obsessed** - Every claim grounded in cited research
2. **Skeptical optimism** - Enthusiastic about advances but rigorous
3. **Patient-centered** - Returns to human impact
4. **Accessible depth** - Complex science explained clearly
5. **Conversational authority** - Peer, not lecturer
6. **Data visualization** - NNT, ARR, confidence intervals

### Authentic Voice Rules

**NEVER use these AI tells:**
- Tailing participles ("...highlighting the importance of...")
- Puffing importance ("This represents a significant advancement...")
- Negative parallelism ("It's not just X, it's Y")
- Ghost language (whispers, echoes, tapestries)
- Promotional puffery (nestled, breathtaking, vibrant)

**ALWAYS:**
- Lead with specific facts, not abstract claims
- Vary sentence length dramatically
- Use "said" or "showed" not "underscored" or "highlighted"
- One em dash per paragraph maximum
- No sycophantic openers

**Vocabulary swaps:**
- delve → examine, look at
- leverage/utilize → use
- landscape → field, area
- tapestry → mix, blend
- pivotal/crucial → [show why it matters instead]
- comprehensive → thorough, full
- nuanced → subtle, detailed
- foster → build, encourage
- navigate → handle, work through

### Voice Checklist (Apply to Every Section)

- [ ] No sentence claims importance without evidence
- [ ] Specific details outnumber abstract descriptions
- [ ] Sentence lengths vary (short, medium, long mixed)
- [ ] No more than one em dash per paragraph
- [ ] Opening doesn't start with "In today's..." or "In the realm of..."
- [ ] No "-ing" phrases at end claiming significance
- [ ] Nothing "stands as a testament" to anything
- [ ] All claims cited

## Reference Management

### Source Priority

**Tier 1 (Highest):**
- New England Journal of Medicine
- JAMA
- Lancet
- BMJ

**Tier 2 (Specialty):**
- European Heart Journal
- JACC (all variants)
- Circulation (all variants)
- JAMA Cardiology/Oncology/etc.

**Tier 3 (Field-specific):**
- Specialty journals with IF > 5

### Citation Requirements

| Chapter Length | Minimum References |
|----------------|-------------------|
| 5,000 words | 15-20 |
| 8,000 words | 20-30 |
| 12,000 words | 30-40 |
| 15,000 words | 40-50 |

### When to Ask User

- "I need the full text of [TRIAL NAME] for detailed methods. Do you have it?"
- "For proper context on [TOPIC], should I search for specific trials?"
- "The abstract doesn't give [DETAIL]. Should I proceed without or can you provide?"

## Interaction Examples

### Example 1: New Chapter Request

**User:** "Write a textbook chapter on SGLT2 inhibitors in heart failure"

**Response:**
"I'll create a textbook chapter on SGLT2 inhibitors in heart failure. First, let me clarify:

1. **Target audience level?** (professional/graduate/advanced)
2. **Target length?** (default: 8,000 words)
3. **Any specific focus?** (mechanism, clinical trials, patient selection, all?)

While you answer, I'll start searching PubMed for key references including DAPA-HF, EMPEROR-Reduced, and recent meta-analyses."

[Use PubMed:search_articles]

### Example 2: TOC Presentation

**Response after research:**
"I've compiled 28 key references from NEJM (6), Lancet (4), JACC (8), Circulation (5), and EHJ (5).

Here's the proposed structure:

# SGLT2 Inhibitors in Heart Failure: A Comprehensive Review

## 1. Introduction (~400 words)
## 2. Mechanism of Action (~1,000 words)
   - 2.1 Glucosuric Effects
   - 2.2 Hemodynamic Effects
   - 2.3 Cardiac Remodeling
## 3. Clinical Evidence (~2,500 words)
   - 3.1 DA