@research-copilot/plugin 1.1.17 → 1.1.19

package/dist/skills/research-proposal/references/LITERATURE_WORKFLOW.md

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+# Literature Collection Workflow
+
+Guide for gathering relevant literature during research proposal generation.
+
+---
+
+## Overview
+
+```
+┌─────────────────────────────────────────────────────────────────────────┐
+│                      Literature Source Strategy                          │
+├─────────────────────────────────────────────────────────────────────────┤
+│                                                                         │
+│  ┌──────────────┐   ┌──────────────────┐   ┌─────────────────────────┐ │
+│  │  WebSearch   │   │   Open Access    │   │    Zotero MCP           │ │
+│  │              │   │                  │   │    (User Library)       │ │
+│  │  • Trends    │   │  • arXiv         │   │                         │ │
+│  │  • News      │   │  • PubMed        │   │  • Full-text papers     │ │
+│  │  • Reviews   │   │  • bioRxiv       │   │  • User annotations     │ │
+│  │  • General   │   │  • SSRN          │   │  • User notes           │ │
+│  │    info      │   │  • Google Scholar│   │  • Organized refs       │ │
+│  └──────────────┘   └──────────────────┘   └─────────────────────────┘ │
+│         │                    │                         │               │
+│         └────────────────────┴─────────────────────────┘               │
+│                              │                                          │
+│                    ┌─────────▼─────────┐                               │
+│                    │  Synthesize into  │                               │
+│                    │  Proposal Sections│                               │
+│                    └───────────────────┘                               │
+└─────────────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## Phase 1: Initial Reconnaissance with WebSearch
+
+### Purpose
+- Understand current landscape
+- Identify key researchers and institutions
+- Find recent reviews and meta-analyses
+- Discover emerging trends
+
+### Search Strategies
+
+#### Broad Overview Searches
+```
+Queries:
+- "{topic} systematic review 2024 2025"
+- "{topic} state of the art"
+- "{topic} research trends"
+- "{topic} future directions"
+```
+
+#### Finding Key Papers
+```
+Queries:
+- "{topic} seminal paper"
+- "{topic} landmark study"
+- "{topic} highly cited"
+- "best papers {topic} {year}"
+```
+
+#### Identifying Gaps
+```
+Queries:
+- "{topic} limitations"
+- "{topic} challenges"
+- "{topic} open problems"
+- "{topic} future research"
+```
+
+#### Methodology Discovery
+```
+Queries:
+- "{topic} methodology"
+- "{topic} research methods"
+- "how to study {phenomenon}"
+- "{method} for {topic}"
+```
+
+### Extracting Information from Web Results
+
+When processing web search results, extract:
+1. **Key findings** - Main results and conclusions
+2. **Authors/Institutions** - Who is working on this
+3. **Timeline** - When major advances occurred
+4. **Terminology** - Field-specific vocabulary
+5. **Controversies** - Debates and disagreements
+6. **Open questions** - Identified gaps
+
+---
+
+## Phase 2: Open Access Sources
+
+### arXiv (STEM, CS, Physics, Math)
+```
+Access: https://arxiv.org/
+Search: https://arxiv.org/search/?query={topic}
+
+Categories:
+- cs.AI - Artificial Intelligence
+- cs.LG - Machine Learning
+- cs.CV - Computer Vision
+- stat.ML - Statistics/ML
+- physics.* - Various physics
+- math.* - Various math
+```
+
+### PubMed (Biomedical, Life Sciences)
+```
+Access: https://pubmed.ncbi.nlm.nih.gov/
+Search: https://pubmed.ncbi.nlm.nih.gov/?term={topic}
+
+Filters useful:
+- Free full text
+- Review articles
+- Publication date range
+- Article type
+```
+
+### bioRxiv/medRxiv (Biology/Medicine Preprints)
+```
+Access: https://www.biorxiv.org/ and https://www.medrxiv.org/
+Note: Preprints, not peer-reviewed
+Use for: Most recent findings, ongoing research
+```
+
+### SSRN (Social Sciences, Economics)
+```
+Access: https://www.ssrn.com/
+Strength: Working papers, business/economics/law
+```
+
+### Google Scholar
+```
+Access: https://scholar.google.com/
+Features:
+- Citation counts
+- Related articles
+- Author profiles
+- "Cited by" links
+```
+
+### Open Access Journals
+```
+PLOS ONE: https://journals.plos.org/plosone/
+Nature Communications: https://www.nature.com/ncomms/
+Scientific Reports: https://www.nature.com/srep/
+```
+
+---
+
+## Phase 3: Zotero MCP Integration
+
+### Prerequisites
+- User must have Zotero installed and configured
+- Zotero MCP server must be running
+- User should have uploaded relevant papers to their library
+
+### Initial Reminder to User
+
+```
+Before we proceed with literature collection, please ensure:
+
+1. Your Zotero library contains relevant papers for this research topic
+2. If you have specific papers you want referenced, please add them to Zotero
+3. Papers with full-text PDFs attached will be most useful
+
+If you haven't prepared your Zotero library yet, I can proceed with open-access
+sources and web searches, then you can add Zotero papers later.
+```
+
+### Zotero MCP Tool Usage
+
+#### Search User's Library
+
+**Basic Keyword Search:**
+```
+Tool: mcp__zotero__zotero_search_items
+Parameters:
+  query: "{research topic keywords}"
+
+Example:
+  query: "deep learning medical imaging"
+```
+
+**Advanced Search:**
+```
+Tool: mcp__zotero__zotero_advanced_search
+Parameters:
+  conditions: based on:
+    - title contains {keyword}
+    - author contains {name}
+    - date > {year}
+    - tag is {tag}
+
+Example:
+  conditions: [
+    {"field": "title", "operator": "contains", "value": "transformer"},
+    {"field": "date", "operator": ">", "value": "2022"}
+  ]
+```
+
+**Semantic Search (if indexed):**
+```
+Tool: mcp__zotero__zotero_semantic_search
+Parameters:
+  query: "{natural language research question}"
+
+Example:
+  query: "What methods are used for detecting cardiac abnormalities in ECG signals?"
+```
+
+#### Retrieve Paper Content
+
+**Get Full Text:**
+```
+Tool: mcp__zotero__zotero_get_item_fulltext
+Parameters:
+  item_key: "{key from search results}"
+
+Returns: Full text content of the paper (if PDF attached)
+```
+
+**Get Metadata:**
+```
+Tool: mcp__zotero__zotero_get_item_metadata
+Parameters:
+  item_key: "{key from search results}"
+
+Returns: Title, authors, abstract, journal, year, DOI, etc.
+```
+
+**Get User Annotations:**
+```
+Tool: mcp__zotero__zotero_get_annotations
+Parameters:
+  item_key: "{key from search results}"
+
+Returns: User's highlights and annotations on the paper
+```
+
+**Get User Notes:**
+```
+Tool: mcp__zotero__zotero_get_notes
+Parameters:
+  item_key: "{key from search results}"
+
+Returns: Any notes the user has attached to the paper
+```
+
+### Zotero Workflow Example
+
+```
+Step 1: Search for papers on the topic
+> zotero_search_items(query="machine learning cardiac diagnosis")
+
+Step 2: From results, identify most relevant papers (by title, year)
+
+Step 3: Get full text of key papers
+> zotero_get_item_fulltext(item_key="ABC123")
+
+Step 4: Check for user insights
+> zotero_get_annotations(item_key="ABC123")
+> zotero_get_notes(item_key="ABC123")
+
+Step 5: Get metadata for citation
+> zotero_get_item_metadata(item_key="ABC123")
+```
+
+---
+
+## Phase 4: Literature Organization
+
+### Categorization Framework
+
+Organize collected literature into these categories:
+
+#### 1. Background/Context Papers
+```
+Purpose: Establish the research field
+Content:
+- Historical development
+- Foundational concepts
+- Widely-accepted theories
+Typical age: Can include older seminal works
+```
+
+#### 2. State-of-the-Art Papers
+```
+Purpose: Show current capabilities and methods
+Content:
+- Recent advances
+- Current best practices
+- Latest methodologies
+Typical age: Last 5 years
+```
+
+#### 3. Gap-Identifying Papers
+```
+Purpose: Support the research gap argument
+Content:
+- Limitations identified by others
+- Calls for future research
+- Reviews noting missing areas
+Typical age: Recent (last 3-5 years)
+```
+
+#### 4. Methodology Papers
+```
+Purpose: Justify and detail methods
+Content:
+- Original method descriptions
+- Validation studies
+- Application examples
+Typical age: Varies; cite original sources
+```
+
+#### 5. Comparative/Related Work
+```
+Purpose: Position the research
+Content:
+- Similar approaches
+- Alternative solutions
+- Adjacent research areas
+Typical age: Recent preferred
+```
+
+### Documentation Template
+
+```markdown
+## Literature Collection Summary
+
+### Background/Context (n papers)
+| Citation | Key Points | Use In |
+|----------|------------|--------|
+| Author (Year) | Main finding | Introduction |
+
+### State-of-the-Art (n papers)
+| Citation | Key Points | Use In |
+|----------|------------|--------|
+| Author (Year) | Current best method | Lit Review |
+
+### Gap-Identifying (n papers)
+| Citation | Identified Gap | Use In |
+|----------|----------------|--------|
+| Author (Year) | "Future work should..." | Lit Review |
+
+### Methodology (n papers)
+| Citation | Method | Use In |
+|----------|--------|--------|
+| Author (Year) | Description of approach | Methodology |
+
+### Related Work (n papers)
+| Citation | Relation | Use In |
+|----------|----------|--------|
+| Author (Year) | Similar but different scope | Lit Review |
+```
+
+---
+
+## Phase 5: Citation Preparation
+
+### Information to Collect
+
+For each paper, capture:
+
+```
+- Authors (full names)
+- Year of publication
+- Title
+- Journal/Conference/Publisher
+- Volume/Issue (if applicable)
+- Pages (if applicable)
+- DOI or URL
+- Key findings (for citing)
+- Relevant quotes (with page numbers)
+```
+
+### Citation Format Examples
+
+#### APA 7th Edition
+```
+Smith, J. A., & Jones, B. C. (2024). Title of article in sentence case.
+    Journal Name in Title Case, 15(3), 123-145. https://doi.org/10.xxxx
+
+Multi-author (3+):
+Chen, X., Wang, Y., Liu, Z., & Zhang, W. (2024). Article title.
+    Journal, 10(2), 45-67. https://doi.org/10.xxxx
+
+In-text:
+(Smith & Jones, 2024)
+(Chen et al., 2024)
+```
+
+#### MLA 9th Edition
+```
+Smith, John A., and Barbara C. Jones. "Article Title Here." Journal Name,
+    vol. 15, no. 3, 2024, pp. 123-145.
+
+In-text:
+(Smith and Jones 128)
+```
+
+#### Chicago Author-Date
+```
+Smith, John A., and Barbara C. Jones. 2024. "Article Title Here."
+    Journal Name 15 (3): 123-145. https://doi.org/10.xxxx
+
+In-text:
+(Smith and Jones 2024, 128)
+```
+
+---
+
+## Handling Different Scenarios
+
+### Scenario 1: Rich Zotero Library
+```
+User has extensive Zotero collection relevant to topic.
+
+Strategy:
+1. Start with Zotero semantic search
+2. Get annotations/notes for user insights
+3. Supplement with web search for recent news/trends
+4. Use user's existing organization (collections, tags)
+```
+
+### Scenario 2: Empty or Sparse Zotero Library
+```
+User has no relevant papers in Zotero.
+
+Strategy:
+1. Inform user of limitation
+2. Rely on WebSearch and open-access sources
+3. Provide clear citations for open-access papers
+4. Suggest key papers user might add to Zotero
+```
+
+### Scenario 3: Very New Topic
+```
+Limited existing literature available.
+
+Strategy:
+1. Focus on foundational/adjacent literature
+2. Emphasize why topic is emerging
+3. Include recent conference papers/preprints
+4. Frame proposal as pioneering work
+```
+
+### Scenario 4: Interdisciplinary Topic
+```
+Topic spans multiple fields.
+
+Strategy:
+1. Search across domain-specific databases
+2. Identify bridging papers
+3. Balance literature from each field
+4. Address methodological borrowing
+```
+
+---
+
+## Quality Checks for Literature
+
+### Coverage Check
+- [ ] Seminal/foundational works included
+- [ ] Recent papers (last 5 years) represented
+- [ ] Multiple perspectives/approaches covered
+- [ ] Key researchers in field cited
+- [ ] Geographic/institutional diversity (if relevant)
+
+### Relevance Check
+- [ ] Each paper directly supports a claim
+- [ ] No tangential citations
+- [ ] Gap papers specifically identify the gap
+- [ ] Method papers describe the methods used
+
+### Balance Check
+- [ ] Not over-reliant on single author/lab
+- [ ] Mix of empirical and theoretical works
+- [ ] Both supporting and challenging views
+- [ ] Appropriate review-to-primary ratio
+
+### Recency Check
+- [ ] ~80% from last 5 years
+- [ ] Latest advances included
+- [ ] No outdated methods cited as current
+- [ ] Historical context appropriately old
+
+---
+
+## Troubleshooting
+
+### "No results found in Zotero"
+```
+Solutions:
+1. Try broader search terms
+2. Check if papers have been uploaded with full text
+3. Verify MCP connection is working
+4. Ask user to add relevant papers
+```
+
+### "WebSearch returns low-quality results"
+```
+Solutions:
+1. Add site filters (site:nature.com, site:arxiv.org)
+2. Use more specific terminology
+3. Include author names if known
+4. Add year constraints
+```
+
+### "Cannot access full text"
+```
+Solutions:
+1. Check open-access repositories (arXiv, PubMed Central)
+2. Use metadata/abstract only
+3. Ask user to obtain and add to Zotero
+4. Note limitation in proposal
+```
+
+### "Too much literature found"
+```
+Solutions:
+1. Prioritize by citation count
+2. Filter by publication venue quality
+3. Focus on most recent within each category
+4. Limit to papers directly supporting claims
+```