@research-copilot/plugin 1.1.17 → 1.1.19

package/dist/skills/research-proposal/SKILL.md

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+---
+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