LITERATURE_WORKFLOW.md 14 KB
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:
- Key findings - Main results and conclusions
- Authors/Institutions - Who is working on this
- Timeline - When major advances occurred
- Terminology - Field-specific vocabulary
- Controversies - Debates and disagreements
- 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
## 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