Research Ideation

3. Gap Analysis

Systematically identify and evaluate research gaps:

• Literature gaps: Identify topics or questions not yet sufficiently studied
• Methodological gaps: Discover limitations and improvement opportunities in existing methods
• Application gaps: Identify opportunities for theory-to-practice transfer
• Interdisciplinary gaps: Discover research opportunities at the intersection of different fields
• Temporal gaps: Identify new research needs arising from changes over time

Analysis Dimensions:

• Coverage of research topics
• Comparison of strengths and weaknesses of existing methods
• Completeness of experimental setups
• Availability of datasets and benchmarks
• Gap between theory and practice

4. Research Question Definition

Formulate specific research questions based on literature analysis:

• Identify research gaps and opportunities
• Apply SMART principles to formulate questions
• Evaluate importance, novelty, and feasibility
• Define research objectives and expected contributions

5. Method Selection

Select appropriate research methods:

• Analyze strengths and weaknesses of existing methods
• Evaluate method applicability
• Identify required technologies and resources
• Consider method feasibility

6. Research Planning

Develop detailed research plans:

• Plan research timeline
• Define milestones and deliverables
• Identify potential risks
• Assess resource requirements

When to Use

Scenarios for This Skill

Use the research-ideation skill in the following situations:

1. Starting a new research project - Have research interests but no clear research question yet
2. Literature review - Need to systematically understand a research field
3. Research question formulation - Need to transform vague ideas into specific research questions
4. Method selection - Need to choose appropriate research methods and technical approaches
5. Research planning - Need to plan research timeline and resources

Typical Workflow

Research interest → Idea brainstorming (5W1H) → Literature review → Gap analysis → Define question → Select method → Create plan

Output Files:

• literature-review.md - Structured literature review
• research-proposal.md - Research proposal (including question, method, plan)
• references.bib - References in BibTeX format
• Zotero collection with organized papers and PDFs

Integration with Other Systems

Complete Research Workflow

research-ideation (Research initiation)
    ↓
Experiment execution (completed by user)
    ↓
results-analysis (Results analysis)
    ↓
ml-paper-writing (Paper writing)

Data Flow

• research-ideation output → Guides experiment design and method selection
• Experimental results → results-analysis for statistical analysis
• Analysis results → Related Work and Methods sections of ml-paper-writing

Zotero Integration

Through the Zotero MCP server, the research-ideation workflow automates literature management:

• Paper Discovery: WebSearch finds relevant papers across academic databases
• Auto-Import: Extract DOIs from search results, use add_items_by_doi to add papers with full metadata
• Collection Organization: create_collection creates topic-based collections with standard sub-collections (Core Papers, Methods, Applications, Baselines, To-Read)
• PDF Attachment: find_and_attach_pdfs automatically finds and attaches open-access PDFs via Unpaywall
• Full-Text Reading: get_item_fulltext reads indexed PDF content for analysis and note-taking
• Library Search: search_library and get_collection_items browse existing papers to avoid duplicates

Key Configuration

• Literature search scope: Papers from the last 3 years by default, configurable
• Output format: Markdown format for easy editing and version control
• Citation management: Generates references in BibTeX format
• Zotero collection naming: Research-{topic}-{YYYY} format
• PDF auto-attach: Enabled by default for open-access papers via Unpaywall

Additional Resources

Reference Files

Detailed methodology guides, loaded on demand:

• references/5w1h-framework.md - 5W1H Framework Guide

  • What, Why, Who, When, Where, How — six dimensions
  • Systematic approach to brainstorming research ideas
  • Integration with superpowers:brainstorming
  • Usage examples and best practices

• references/literature-search-strategies.md - Literature Search Strategies

  • Keyword construction techniques
  • Academic database selection (arXiv, Google Scholar)
  • Search tips and screening criteria
  • Paper quality evaluation methods
  • DOI extraction and Zotero auto-import workflow

• references/zotero-integration-guide.md - Zotero MCP Integration Guide

  • Available Zotero MCP tools (browse, add, cite)
  • Collection organization strategy and naming conventions
  • Automated workflow: WebSearch → DOI → Zotero import → PDF attach
  • Full-text reading and structured note-taking
  • Common issues and troubleshooting

• references/gap-analysis-guide.md - Gap Analysis Guide

  • 5 types of Gap Analysis (literature, methodological, application, interdisciplinary, temporal)
  • 5 analysis dimensions
  • Systematic approach to identifying research opportunities
  • Usage examples and best practices

• references/research-question-formulation.md - Research Question Formulation

  • Applying SMART principles
  • Question type classification (exploratory, confirmatory, applied)
  • Evaluation criteria (importance, novelty, feasibility)
  • Defining research objectives and contributions

• references/method-selection-guide.md - Method Selection Guide

  • Common research method classification
  • Method applicability analysis
  • Strengths and weaknesses comparison
  • Resource requirement assessment

• references/research-planning.md - Research Planning

  • Timeline planning methods
  • Milestone definition techniques
  • Risk identification and mitigation
  • Resource allocation strategies

Example Files

Complete working examples:

• examples/example-literature-review.md - Literature Review Example

  • Demonstrates structured literature review format
  • Includes research trend analysis and gap identification

• examples/example-research-proposal.md - Research Proposal Example

  • Demonstrates complete research proposal structure
  • Includes complete examples of question, method, and plan