research-proposal skill

---
name: research-proposal
description: >
  Generate academic research proposals for PhD applications.
  Use when user asks to "write a research proposal", "create PhD proposal",
  "generate research plan", "撰写研究计划", "写博士申请", "doctoral proposal",
  or mentions specific research topics for PhD application. Supports STEM,
  humanities, and social sciences with field-specific adaptations.
  Follows Nature Reviews-style academic writing conventions.
  Supports both English and Chinese output based on user preference.
metadata:
  author: user
  version: "1.0.0"
allowed-tools:
  - WebSearch
  - Read
  - Write
  - Edit
  - AskUserQuestion
  - Task
  - Glob
  - Grep
  - mcp__zotero__zotero_search_items
  - mcp__zotero__zotero_get_item_metadata
  - mcp__zotero__zotero_get_item_fulltext
  - mcp__zotero__zotero_get_annotations
  - mcp__zotero__zotero_get_notes
  - mcp__zotero__zotero_search_notes
  - mcp__zotero__zotero_semantic_search
  - mcp__zotero__zotero_advanced_search
---

# Research Proposal Generator

Generate high-quality academic research proposals for PhD applications following Nature Reviews-style academic writing conventions.

## Overview

This skill guides the generation of research proposals through a structured 5-phase workflow:

1. **Requirements Gathering** - Collect research topic, domain, language preferences
2. **Literature Collection** - Gather relevant literature from multiple sources
3. **Outline Generation** - Create structured outline for user approval
4. **Content Writing** - Generate full proposal based on approved outline
5. **Output & Review** - Deliver Markdown file with quality checklist

**Target Output**: 2,000-4,000 words (default ~3,000 words) for PhD applications.

---

## Phase 1: Requirements Gathering

Use `AskUserQuestion` to collect the following information:

### Required Information

1. **Research Topic/Direction**
   - What is the core research question or area?
   - Any specific problems to address?

2. **Academic Domain**
   - STEM (Science, Technology, Engineering, Mathematics)
   - Humanities (History, Philosophy, Literature, Languages)
   - Social Sciences (Sociology, Psychology, Economics, Political Science)

3. **Output Language**
   - English
   - 中文 (Chinese)

4. **Target Word Count**
   - Default: 3,000 words
   - Range: 2,000-4,000 words (humanities may extend to 10,000)

### Optional Information

5. **Target Institution(s)**
   - University/research group names
   - Specific faculty members of interest

6. **Existing Materials**
   - User's prior research or publications
   - Relevant literature already collected in Zotero

### Example Questions

```
Questions to ask the user:

1. "What is your research topic or direction? Please describe the core question or problem you want to investigate."

2. "Which academic domain does your research belong to?"
   - STEM (Science, Technology, Engineering, Mathematics)
   - Humanities (History, Philosophy, Literature)
   - Social Sciences (Sociology, Psychology, Economics)

3. "What language should the proposal be written in?"
   - English
   - 中文 (Chinese)

4. "Do you have a target word count? (Default: ~3,000 words)"

5. "Are you applying to specific institutions or working with particular faculty?"

6. "Have you uploaded relevant literature to your Zotero library that I should reference?"
```

---

## Phase 2: Literature Collection

### Literature Sources Strategy

```
┌─────────────────────────────────────────────────────────┐
│                    Literature Sources                    │
├─────────────────────────────────────────────────────────┤
│  General Info    →  WebSearch (trends, news, reviews)   │
│  Open Access     →  arXiv, PubMed (preprints, OA papers)│
│  Closed Access   →  Zotero MCP (user's uploaded papers) │
└─────────────────────────────────────────────────────────┘
```

### Using WebSearch

Search for:
- Recent review articles and meta-analyses
- Research trends and emerging topics
- News about breakthroughs in the field
- Methodological advances

Example searches:
```
"{topic} systematic review 2024 2025"
"{topic} research trends future directions"
"{topic} methodology recent advances"
```

### Using Zotero MCP

**IMPORTANT**: Remind users to upload relevant closed-access literature to Zotero before starting.

#### Search User's Library

```
# Search by topic keywords
Use: mcp__zotero__zotero_search_items
Parameters: query = "{research topic keywords}"

# Advanced search with filters
Use: mcp__zotero__zotero_advanced_search
Parameters: conditions based on author, title, year, tags

# Semantic search for related papers
Use: mcp__zotero__zotero_semantic_search
Parameters: query = "{research question}"
```

#### Retrieve Paper Content

```
# Get full text content
Use: mcp__zotero__zotero_get_item_fulltext
Parameters: item_key = "{item key from search}"

# Get user's annotations and highlights
Use: mcp__zotero__zotero_get_annotations
Parameters: item_key = "{item key}"

# Get user's notes
Use: mcp__zotero__zotero_get_notes
Parameters: item_key = "{item key}"
```

### Literature Organization

Organize collected literature into categories:
1. **Background/Context** - Foundational papers establishing the field
2. **Current State** - Recent advances and state-of-the-art
3. **Research Gap** - Papers identifying limitations or open questions
4. **Methodology** - Papers with relevant methods to adopt/adapt
5. **Related Work** - Adjacent research areas for comparison

---

## Phase 3: Outline Generation

### Proposal Structure by Domain

Read the reference file for domain-specific guidance:
- `references/STRUCTURE_GUIDE.md` - Detailed section guidelines
- `references/DOMAIN_TEMPLATES.md` - STEM vs Humanities differences

### Standard Outline Template

```markdown
# [Research Title]

## Abstract (150-300 words, 5-10%)
- Research problem summary
- Research questions/objectives
- Methodology overview
- Expected significance

## 1. Introduction (500-800 words, 15-20%)
### 1.1 Background and Context
### 1.2 Problem Statement
### 1.3 Research Questions/Objectives
### 1.4 Scope and Delimitations

## 2. Literature Review (500-1000 words, 20-25%)
### 2.1 Theoretical Framework
### 2.2 Current State of Research
### 2.3 Research Gap Analysis
### 2.4 Positioning of This Study

## 3. Methodology (500-800 words, 20-25%)
### 3.1 Research Design
### 3.2 Data Collection Methods
### 3.3 Data Analysis Approach
### 3.4 Validity and Limitations

## 4. Timeline (200-300 words, 5-10%)
### 4.1 Research Phases
### 4.2 Key Milestones
### 4.3 Gantt Chart (optional)

## 5. Significance and Expected Contributions (200-400 words, 10-15%)
### 5.1 Theoretical Contributions
### 5.2 Practical Implications
### 5.3 Broader Impact

## References (minimum 40 references)
```

**Note**: Do NOT include Appendix sections. All essential content should be integrated into the main body.

### User Confirmation

**CRITICAL**: Present the outline to the user and wait for confirmation before proceeding to content generation.

```
Present the generated outline and ask:

"Here is the proposed outline for your research proposal:

[Display outline with section titles and estimated word counts]

Please review and let me know:
1. Is the overall structure acceptable?
2. Would you like to add, remove, or modify any sections?
3. Should any section receive more/less emphasis?

I will proceed with content generation once you approve the outline."
```

---

## Phase 4: Content Writing

### Writing Style Guidelines

Read and apply: `references/WRITING_STYLE_GUIDE.md`

#### Key Principles

1. **Academic Register**
   - Formal tone, avoid colloquialisms
   - Third person preferred, limited first person plural ("we")
   - Precise terminology

2. **Prose-Based Writing Style** (CRITICAL)

   **AVOID point-by-point enumeration.** Academic proposals should read as flowing, connected prose rather than bulleted lists or numbered items. Use transitional phrases and coherent paragraphs to present ideas.

   | Avoid | Use Instead |
   |-------|-------------|
   | Bullet points listing objectives | Integrated paragraph describing objectives with transitions |
   | Numbered lists of contributions | Narrative prose explaining contributions in context |
   | Tables for methodology steps | Flowing description of research design |

   **When lists ARE appropriate** (use sparingly):
   - Research questions/objectives (as a focused set of 2-4 items)
   - Timeline milestones (where tabular format aids clarity)
   - Technical specifications that require precise enumeration

   **Example transformation:**

   ❌ Poor (point-by-point):
   ```
   The contributions include:
   - Novel segmentation algorithm
   - Multi-modal fusion framework
   - Clinical validation study
   ```

   ✓ Good (prose-based):
   ```
   This research is expected to advance the field through several interconnected
   contributions. First, the development of a novel segmentation algorithm will
   enable automated plaque detection with accuracy surpassing current methods.
   Building on this foundation, a multi-modal fusion framework will integrate
   complementary imaging data to capture plaque characteristics inaccessible to
   any single modality. Finally, rigorous clinical validation will establish
   the prognostic value of these computational biomarkers for predicting
   cardiovascular events.
   ```

3. **Hedging Language** (Academic Caution)

   | Avoid | Use Instead |
   |-------|-------------|
   | "will prove" | "aims to demonstrate" |
   | "definitely" | "likely", "potentially" |
   | "is obvious" | "evidence suggests" |
   | "proves" | "indicates", "demonstrates" |

3. **Sentence Templates**

   **Introducing Background:**
   - "Over the past decade, [X] has emerged as a critical area of..."
   - "Recent advances in [X] have opened new possibilities for..."

   **Identifying Gaps:**
   - "However, [X] remains poorly understood."
   - "Despite these advances, significant challenges persist in..."
   - "A critical gap exists in our understanding of..."

   **Stating Objectives:**
   - "This research aims to address [X] by..."
   - "The primary objective of this study is to..."
   - "This proposal seeks to investigate..."

   **Methodology Justification:**
   - "Building on previous work, this study proposes to..."
   - "This approach was selected because..."
   - "[Method] offers several advantages for studying [X]..."

   **Expected Contributions:**
   - "This work has the potential to advance..."
   - "The findings may contribute to..."
   - "This research could provide insights into..."

4. **Transitions and Connectors**
   - Addition: Moreover, Furthermore, In addition, Additionally
   - Contrast: However, Nevertheless, Conversely, On the other hand
   - Causation: Therefore, Consequently, As a result, Thus
   - Emphasis: Importantly, Notably, Of particular significance
   - Sequence: First, Subsequently, Finally, Following this

5. **Paragraph Structure**
   ```
   Topic Sentence → Supporting Evidence (with citations) → Synthesis/Implications
   ```
   - 4-8 sentences per paragraph
   - Clear logical progression
   - Explicit transitions between paragraphs

### Citation Formatting

Based on domain:
- **STEM**: APA style (Author, Year)
- **Humanities**: MLA or Chicago style
- **Social Sciences**: APA or Chicago style

First mention of abbreviations: "coronary CT angiography (CCTA)"

Integrate citations into text: "Recent studies (Smith et al., 2023; Jones, 2024) have demonstrated..."

### Figure Suggestions

**IMPORTANT**: Include suggestions for figures at appropriate locations throughout the proposal. Figures significantly enhance readability and demonstrate the applicant's ability to communicate complex ideas visually.

#### Figure Placement Guidelines

Insert figure suggestions using the following format:

```markdown
> **[Figure 1 Suggestion]** *Title: Overview of the proposed research framework*
> Content: A flowchart or schematic diagram illustrating the three-phase research
> design, showing data flow from imaging modalities through AI processing to
> clinical outcomes. Include icons for CCTA/IVUS/OCT inputs, deep learning
> modules, and output predictions.
> Recommended style: Clean vector graphics with consistent color scheme.
```

#### Recommended Figure Types by Section

| Section | Suggested Figure Type |
|---------|----------------------|
| **Introduction** | Conceptual diagram showing research scope and positioning |
| **Literature Review** | Timeline of key developments; Taxonomy/classification of existing methods |
| **Methodology** | Research framework flowchart; Network architecture diagram; Data processing pipeline |
| **Timeline** | Gantt chart showing research phases and milestones |
| **Significance** | Impact diagram showing theoretical and practical contributions |

#### Figure Suggestion Principles

1. **Strategic placement**: Suggest 3-5 figures for a 3,000-word proposal
2. **Self-explanatory**: Each figure should convey key information without requiring extensive caption reading
3. **Consistent style**: Recommend unified visual language (colors, fonts, icons)
4. **Professional quality**: Suggest tools (e.g., Adobe Illustrator, draw.io, BioRender for biomedical)
5. **Accessibility**: Recommend colorblind-friendly palettes and sufficient contrast

### Language-Specific Considerations

#### English Output
- Follow standard academic English conventions
- Use British or American English consistently
- Maintain formal register throughout

#### Chinese Output (中文)
- 使用规范学术中文
- 适当使用 hedging 语言:
  - "本研究旨在探讨..." (not "本研究将证明...")
  - "研究结果可能表明..." (not "研究结果必定显示...")
  - "有望推进..." (not "肯定会推进...")
- 保持正式学术语体
- 参考文献格式遵循 GB/T 7714

---

## Phase 5: Output and Review

### File Generation

Generate the proposal as a Markdown file:

```
proposal_{topic_slug}_{YYYY-MM-DD}.md
```

Save to user's working directory or specified location.

### Quality Checklist

Read and apply: `references/QUALITY_CHECKLIST.md`

Verify:

#### Structure
- [ ] All required sections present
- [ ] Word counts within specified ranges
- [ ] Logical flow between sections
- [ ] Clear section headings

#### Content
- [ ] Research questions clearly stated
- [ ] Literature review identifies specific gap
- [ ] Methodology appropriate for research questions
- [ ] Timeline realistic and detailed
- [ ] Significance clearly articulated

#### Academic Style
- [ ] Formal academic tone throughout
- [ ] Appropriate hedging language used
- [ ] Smooth transitions between sections
- [ ] No colloquialisms or informal expressions
- [ ] **Prose-based writing** (minimal bullet points/lists)
- [ ] Lists used ONLY where truly necessary (e.g., research questions, timeline)

#### Figures
- [ ] **3-5 figure suggestions** included at appropriate locations
- [ ] Figure suggestions include title, content description, and style recommendations
- [ ] Figures distributed across sections (not clustered)
- [ ] Each figure serves a clear communicative purpose

#### Citations
- [ ] All claims supported by references
- [ ] Citation format consistent
- [ ] **Minimum 40 references** for PhD proposals
- [ ] Recent literature included (~60% from last 5 years)
- [ ] Seminal/foundational works cited where appropriate
- [ ] Balance across different research groups/institutions

#### Technical
- [ ] No grammatical errors
- [ ] Abbreviations defined on first use
- [ ] Consistent terminology
- [ ] Proper markdown formatting

### Format Conversion Guidance

Provide user with conversion instructions:

```bash
# Convert to Word document
pandoc proposal.md -o proposal.docx

# Convert to PDF (requires LaTeX)
pandoc proposal.md -o proposal.pdf

# Convert to PDF with custom styling
pandoc proposal.md -o proposal.pdf --template=academic.latex
```

---

## Reference Files

This skill uses the following reference documents:

| File | Purpose |
|------|---------|
| `references/STRUCTURE_GUIDE.md` | Detailed section-by-section writing guide |
| `references/DOMAIN_TEMPLATES.md` | STEM vs Humanities structural differences |
| `references/WRITING_STYLE_GUIDE.md` | Nature Reviews academic writing style |
| `references/QUALITY_CHECKLIST.md` | Complete quality verification checklist |
| `references/LITERATURE_WORKFLOW.md` | Literature collection workflow details |
| `assets/proposal_scaffold_en.md` | English template scaffold |
| `assets/proposal_scaffold_zh.md` | Chinese template scaffold |

---

## Workflow Summary

```
┌──────────────────────────────────────────────────────────────────┐
│                    Research Proposal Generation                   │
├──────────────────────────────────────────────────────────────────┤
│                                                                  │
│  Phase 1: Requirements    [Interactive]                          │
│     │     └─ Topic, Domain, Language, Word Count                 │
│     ▼                                                            │
│  Phase 2: Literature      [Automatic]                            │
│     │     └─ WebSearch + Zotero MCP                              │
│     ▼                                                            │
│  Phase 3: Outline         [Interactive - User Approval Required] │
│     │     └─ Generate outline → User confirms → Proceed          │
│     ▼                                                            │
│  Phase 4: Content         [Automatic - One-shot Generation]      │
│     │     └─ Write all sections based on approved outline        │
│     ▼                                                            │
│  Phase 5: Output          [Delivery]                             │
│           └─ Markdown file + Quality checklist + Conversion tips │
│                                                                  │
└──────────────────────────────────────────────────────────────────┘
```

---

## Error Handling

### No Zotero Literature Found
If user's Zotero library has no relevant papers:
1. Inform user of the limitation
2. Rely more heavily on WebSearch for open-access sources
3. Suggest user upload relevant papers and retry

### Insufficient Information
If topic is too vague:
1. Ask clarifying questions about specific aspects
2. Suggest narrowing the research scope
3. Provide examples of well-defined research questions

### Word Count Constraints
If content exceeds target:
1. Prioritize essential sections (Introduction, Methodology)
2. Condense literature review to key points
3. Offer expanded version as separate file

---

## Notes

- This skill is designed specifically for **PhD applications**
- Default output is approximately **3,000 words**
- Always **confirm outline with user** before content generation
- Follow **Nature Reviews-style** academic writing conventions
- Support **both English and Chinese** output
- **Minimum 40 references** required for comprehensive literature coverage
- **Include figure suggestions** at appropriate locations (3-5 figures recommended)
- **NO appendices** in the output - keep all content in main body sections
- **Prefer flowing prose** over bullet points and numbered lists