scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md

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+# Google Scholar Search Guide
+
+Comprehensive guide to searching Google Scholar for academic papers, including advanced search operators, filtering strategies, and metadata extraction.
+
+## Overview
+
+Google Scholar provides the most comprehensive coverage of academic literature across all disciplines:
+- **Coverage**: 100+ million scholarly documents
+- **Scope**: All academic disciplines
+- **Content types**: Journal articles, books, theses, conference papers, preprints, patents, court opinions
+- **Citation tracking**: "Cited by" links for forward citation tracking
+- **Accessibility**: Free to use, no account required
+
+## Basic Search
+
+### Simple Keyword Search
+
+Search for papers containing specific terms anywhere in the document (title, abstract, full text):
+
+```
+CRISPR gene editing
+machine learning protein folding
+climate change impact agriculture
+quantum computing algorithms
+```
+
+**Tips**:
+- Use specific technical terms
+- Include key acronyms and abbreviations
+- Start broad, then refine
+- Check spelling of technical terms
+
+### Exact Phrase Search
+
+Use quotation marks to search for exact phrases:
+
+```
+"deep learning"
+"CRISPR-Cas9"
+"systematic review"
+"randomized controlled trial"
+```
+
+**When to use**:
+- Technical terms that must appear together
+- Proper names
+- Specific methodologies
+- Exact titles
+
+## Advanced Search Operators
+
+### Author Search
+
+Find papers by specific authors:
+
+```
+author:LeCun
+author:"Geoffrey Hinton"
+author:Church synthetic biology
+```
+
+**Variations**:
+- Single last name: `author:Smith`
+- Full name in quotes: `author:"Jane Smith"`
+- Author + topic: `author:Doudna CRISPR`
+
+**Tips**:
+- Authors may publish under different name variations
+- Try with and without middle initials
+- Consider name changes (marriage, etc.)
+- Use quotation marks for full names
+
+### Title Search
+
+Search only in article titles:
+
+```
+intitle:transformer
+intitle:"attention mechanism"
+intitle:review climate change
+```
+
+**Use cases**:
+- Finding papers specifically about a topic
+- More precise than full-text search
+- Reduces irrelevant results
+- Good for finding reviews or methods
+
+### Source (Journal) Search
+
+Search within specific journals or conferences:
+
+```
+source:Nature
+source:"Nature Communications"
+source:NeurIPS
+source:"Journal of Machine Learning Research"
+```
+
+**Applications**:
+- Track publications in top-tier venues
+- Find papers in specialized journals
+- Identify conference-specific work
+- Verify publication venue
+
+### Exclusion Operator
+
+Exclude terms from results:
+
+```
+machine learning -survey
+CRISPR -patent
+climate change -news
+deep learning -tutorial -review
+```
+
+**Common exclusions**:
+- `-survey`: Exclude survey papers
+- `-review`: Exclude review articles
+- `-patent`: Exclude patents
+- `-book`: Exclude books
+- `-news`: Exclude news articles
+- `-tutorial`: Exclude tutorials
+
+### OR Operator
+
+Search for papers containing any of multiple terms:
+
+```
+"machine learning" OR "deep learning"
+CRISPR OR "gene editing"
+"climate change" OR "global warming"
+```
+
+**Best practices**:
+- OR must be uppercase
+- Combine synonyms
+- Include acronyms and spelled-out versions
+- Use with exact phrases
+
+### Wildcard Search
+
+Use asterisk (*) as wildcard for unknown words:
+
+```
+"machine * learning"
+"CRISPR * editing"
+"* neural network"
+```
+
+**Note**: Limited wildcard support in Google Scholar compared to other databases.
+
+## Advanced Filtering
+
+### Year Range
+
+Filter by publication year:
+
+**Using interface**:
+- Click "Since [year]" on left sidebar
+- Select custom range
+
+**Using search operators**:
+```
+# Not directly in search query
+# Use interface or URL parameters
+```
+
+**In script**:
+```bash
+python scripts/search_google_scholar.py "quantum computing" \
+  --year-start 2020 \
+  --year-end 2024
+```
+
+### Sorting Options
+
+**By relevance** (default):
+- Google's algorithm determines relevance
+- Considers citations, author reputation, publication venue
+- Generally good for most searches
+
+**By date**:
+- Most recent papers first
+- Good for fast-moving fields
+- May miss highly cited older papers
+- Click "Sort by date" in interface
+
+**By citation count** (via script):
+```bash
+python scripts/search_google_scholar.py "transformers" \
+  --sort-by citations \
+  --limit 50
+```
+
+### Language Filtering
+
+**In interface**:
+- Settings → Languages
+- Select preferred languages
+
+**Default**: English and papers with English abstracts
+
+## Search Strategies
+
+### Finding Seminal Papers
+
+Identify highly influential papers in a field:
+
+1. **Search by topic** with broad terms
+2. **Sort by citations** (most cited first)
+3. **Look for review articles** for comprehensive overviews
+4. **Check publication dates** for foundational vs recent work
+
+**Example**:
+```
+"generative adversarial networks"
+# Sort by citations
+# Top results: original GAN paper (Goodfellow et al., 2014), key variants
+```
+
+### Finding Recent Work
+
+Stay current with latest research:
+
+1. **Search by topic**
+2. **Filter to recent years** (last 1-2 years)
+3. **Sort by date** for newest first
+4. **Set up alerts** for ongoing tracking
+
+**Example**:
+```bash
+python scripts/search_google_scholar.py "AlphaFold protein structure" \
+  --year-start 2023 \
+  --year-end 2024 \
+  --limit 50
+```
+
+### Finding Review Articles
+
+Get comprehensive overviews of a field:
+
+```
+intitle:review "machine learning"
+"systematic review" CRISPR
+intitle:survey "natural language processing"
+```
+
+**Indicators**:
+- "review", "survey", "perspective" in title
+- Often highly cited
+- Published in review journals (Nature Reviews, Trends, etc.)
+- Comprehensive reference lists
+
+### Citation Chain Search
+
+**Forward citations** (papers citing a key paper):
+1. Find seminal paper
+2. Click "Cited by X"
+3. See all papers that cite it
+4. Identify how field has developed
+
+**Backward citations** (references in a key paper):
+1. Find recent review or important paper
+2. Check its reference list
+3. Identify foundational work
+4. Trace development of ideas
+
+**Example workflow**:
+```
+# Find original transformer paper
+"Attention is all you need" author:Vaswani
+
+# Check "Cited by 120,000+"
+# See evolution: BERT, GPT, T5, etc.
+
+# Check references in original paper
+# Find RNN, LSTM, attention mechanism origins
+```
+
+### Comprehensive Literature Search
+
+For thorough coverage (e.g., systematic reviews):
+
+1. **Generate synonym list**:
+   - Main terms + alternatives
+   - Acronyms + spelled out
+   - US vs UK spelling
+
+2. **Use OR operators**:
+   ```
+   ("machine learning" OR "deep learning" OR "neural networks")
+   ```
+
+3. **Combine multiple concepts**:
+   ```
+   ("machine learning" OR "deep learning") ("drug discovery" OR "drug development")
+   ```
+
+4. **Search without date filters** initially:
+   - Get total landscape
+   - Filter later if too many results
+
+5. **Export results** for systematic analysis:
+   ```bash
+   python scripts/search_google_scholar.py \
+     '"machine learning" OR "deep learning" drug discovery' \
+     --limit 500 \
+     --output comprehensive_search.json
+   ```
+
+## Extracting Citation Information
+
+### From Google Scholar Results Page
+
+Each result shows:
+- **Title**: Paper title (linked to full text if available)
+- **Authors**: Author list (often truncated)
+- **Source**: Journal/conference, year, publisher
+- **Cited by**: Number of citations + link to citing papers
+- **Related articles**: Link to similar papers
+- **All versions**: Different versions of the same paper
+
+### Export Options
+
+**Manual export**:
+1. Click "Cite" under paper
+2. Select BibTeX format
+3. Copy citation
+
+**Limitations**:
+- One paper at a time
+- Manual process
+- Time-consuming for many papers
+
+**Automated export** (using script):
+```bash
+# Search and export to BibTeX
+python scripts/search_google_scholar.py "quantum computing" \
+  --limit 50 \
+  --format bibtex \
+  --output quantum_papers.bib
+```
+
+### Metadata Available
+
+From Google Scholar you can typically extract:
+- Title
+- Authors (may be incomplete)
+- Year
+- Source (journal/conference)
+- Citation count
+- Link to full text (when available)
+- Link to PDF (when available)
+
+**Note**: Metadata quality varies:
+- Some fields may be missing
+- Author names may be incomplete
+- Need to verify with DOI lookup for accuracy
+
+## Rate Limiting and Access
+
+### Rate Limits
+
+Google Scholar has rate limiting to prevent automated scraping:
+
+**Symptoms of rate limiting**:
+- CAPTCHA challenges
+- Temporary IP blocks
+- 429 "Too Many Requests" errors
+
+**Best practices**:
+1. **Add delays between requests**: 2-5 seconds minimum
+2. **Limit query volume**: Don't search hundreds of queries rapidly
+3. **Use scholarly library**: Handles rate limiting automatically
+4. **Rotate User-Agents**: Appear as different browsers
+5. **Consider proxies**: For large-scale searches (use ethically)
+
+**In our scripts**:
+```python
+# Automatic rate limiting built in
+time.sleep(random.uniform(3, 7))  # Random delay 3-7 seconds
+```
+
+### Ethical Considerations
+
+**DO**:
+- Respect rate limits
+- Use reasonable delays
+- Cache results (don't re-query)
+- Use official APIs when available
+- Attribute data properly
+
+**DON'T**:
+- Scrape aggressively
+- Use multiple IPs to bypass limits
+- Violate terms of service
+- Burden servers unnecessarily
+- Use data commercially without permission
+
+### Institutional Access
+
+**Benefits of institutional access**:
+- Access to full-text PDFs through library subscriptions
+- Better download capabilities
+- Integration with library systems
+- Link resolver to full text
+
+**Setup**:
+- Google Scholar → Settings → Library links
+- Add your institution
+- Links appear in search results
+
+## Tips and Best Practices
+
+### Search Optimization
+
+1. **Start simple, then refine**:
+   ```
+   # Too specific initially
+   intitle:"deep learning" intitle:review source:Nature 2023..2024
+   
+   # Better approach
+   deep learning review
+   # Review results
+   # Add intitle:, source:, year filters as needed
+   ```
+
+2. **Use multiple search strategies**:
+   - Keyword search
+   - Author search for known experts
+   - Citation chaining from key papers
+   - Source search in top journals
+
+3. **Check spelling and variations**:
+   - Color vs colour
+   - Optimization vs optimisation
+   - Tumor vs tumour
+   - Try common misspellings if few results
+
+4. **Combine operators strategically**:
+   ```
+   # Good combination
+   author:Church intitle:"synthetic biology" 2015..2024
+   
+   # Find reviews by specific author on topic in recent years
+   ```
+
+### Result Evaluation
+
+1. **Check citation counts**:
+   - High citations indicate influence
+   - Recent papers may have low citations but be important
+   - Citation counts vary by field
+
+2. **Verify publication venue**:
+   - Peer-reviewed journals vs preprints
+   - Conference proceedings
+   - Book chapters
+   - Technical reports
+
+3. **Check for full text access**:
+   - [PDF] link on right side
+   - "All X versions" may have open access version
+   - Check institutional access
+   - Try author's website or ResearchGate
+
+4. **Look for review articles**:
+   - Comprehensive overviews
+   - Good starting point for new topics
+   - Extensive reference lists
+
+### Managing Results
+
+1. **Use citation manager integration**:
+   - Export to BibTeX
+   - Import to Zotero, Mendeley, EndNote
+   - Maintain organized library
+
+2. **Set up alerts** for ongoing research:
+   - Google Scholar → Alerts
+   - Get emails for new papers matching query
+   - Track specific authors or topics
+
+3. **Create collections**:
+   - Save papers to Google Scholar Library
+   - Organize by project or topic
+   - Add labels and notes
+
+4. **Export systematically**:
+   ```bash
+   # Save search results for later analysis
+   python scripts/search_google_scholar.py "your topic" \
+     --output topic_papers.json
+   
+   # Can re-process later without re-searching
+   python scripts/extract_metadata.py \
+     --input topic_papers.json \
+     --output topic_refs.bib
+   ```
+
+## Advanced Techniques
+
+### Boolean Logic Combinations
+
+Combine multiple operators for precise searches:
+
+```
+# Highly cited reviews on specific topic by known authors
+intitle:review "machine learning" ("drug discovery" OR "drug development")
+author:Horvath OR author:Bengio 2020..2024
+
+# Method papers excluding reviews
+intitle:method "protein folding" -review -survey
+
+# Papers in top journals only
+("Nature" OR "Science" OR "Cell") CRISPR 2022..2024
+```
+
+### Finding Open Access Papers
+
+```
+# Search with generic terms
+machine learning
+
+# Filter by "All versions" which often includes preprints
+# Look for green [PDF] links (often open access)
+# Check arXiv, bioRxiv versions
+```
+
+**In script**:
+```bash
+python scripts/search_google_scholar.py "topic" \
+  --open-access-only \
+  --output open_access_papers.json
+```
+
+### Tracking Research Impact
+
+**For a specific paper**:
+1. Find the paper
+2. Click "Cited by X"
+3. Analyze citing papers:
+   - How is it being used?
+   - What fields cite it?
+   - Recent vs older citations?
+
+**For an author**:
+1. Search `author:LastName`
+2. Check h-index and i10-index
+3. View citation history graph
+4. Identify most influential papers
+
+**For a topic**:
+1. Search topic
+2. Sort by citations
+3. Identify seminal papers (highly cited, older)
+4. Check recent highly-cited papers (emerging important work)
+
+### Finding Preprints and Early Work
+
+```
+# arXiv papers
+source:arxiv "deep learning"
+
+# bioRxiv papers
+source:biorxiv CRISPR
+
+# All preprint servers
+("arxiv" OR "biorxiv" OR "medrxiv") your topic
+```
+
+**Note**: Preprints are not peer-reviewed. Always check if published version exists.
+
+## Common Issues and Solutions
+
+### Too Many Results
+
+**Problem**: Search returns 100,000+ results, overwhelming.
+
+**Solutions**:
+1. Add more specific terms
+2. Use `intitle:` to search only titles
+3. Filter by recent years
+4. Add exclusions (e.g., `-review`)
+5. Search within specific journals
+
+### Too Few Results
+
+**Problem**: Search returns 0-10 results, suspiciously few.
+
+**Solutions**:
+1. Remove restrictive operators
+2. Try synonyms and related terms
+3. Check spelling
+4. Broaden year range
+5. Use OR for alternative terms
+
+### Irrelevant Results
+
+**Problem**: Results don't match intent.
+
+**Solutions**:
+1. Use exact phrases with quotes
+2. Add more specific context terms
+3. Use `intitle:` for title-only search
+4. Exclude common irrelevant terms
+5. Combine multiple specific terms
+
+### CAPTCHA or Rate Limiting
+
+**Problem**: Google Scholar shows CAPTCHA or blocks access.
+
+**Solutions**:
+1. Wait several minutes before continuing
+2. Reduce query frequency
+3. Use longer delays in scripts (5-10 seconds)
+4. Switch to different IP/network
+5. Consider using institutional access
+
+### Missing Metadata
+
+**Problem**: Author names, year, or venue missing from results.
+
+**Solutions**:
+1. Click through to see full details
+2. Check "All versions" for better metadata
+3. Look up by DOI if available
+4. Extract metadata from CrossRef/PubMed instead
+5. Manually verify from paper PDF
+
+### Duplicate Results
+
+**Problem**: Same paper appears multiple times.
+
+**Solutions**:
+1. Click "All X versions" to see consolidated view
+2. Choose version with best metadata
+3. Use deduplication in post-processing:
+   ```bash
+   python scripts/format_bibtex.py results.bib \
+     --deduplicate \
+     --output clean_results.bib
+   ```
+
+## Integration with Scripts
+
+### search_google_scholar.py Usage
+
+**Basic search**:
+```bash
+python scripts/search_google_scholar.py "machine learning drug discovery"
+```
+
+**With year filter**:
+```bash
+python scripts/search_google_scholar.py "CRISPR" \
+  --year-start 2020 \
+  --year-end 2024 \
+  --limit 100
+```
+
+**Sort by citations**:
+```bash
+python scripts/search_google_scholar.py "transformers" \
+  --sort-by citations \
+  --limit 50
+```
+
+**Export to BibTeX**:
+```bash
+python scripts/search_google_scholar.py "quantum computing" \
+  --format bibtex \
+  --output quantum.bib
+```
+
+**Export to JSON for later processing**:
+```bash
+python scripts/search_google_scholar.py "topic" \
+  --format json \
+  --output results.json
+
+# Later: extract full metadata
+python scripts/extract_metadata.py \
+  --input results.json \
+  --output references.bib
+```
+
+### Batch Searching
+
+For multiple topics:
+
+```bash
+# Create file with search queries (queries.txt)
+# One query per line
+
+# Search each query
+while read query; do
+  python scripts/search_google_scholar.py "$query" \
+    --limit 50 \
+    --output "${query// /_}.json"
+  sleep 10  # Delay between queries
+done < queries.txt
+```
+
+## Summary
+
+Google Scholar is the most comprehensive academic search engine, providing:
+
+✓ **Broad coverage**: All disciplines, 100M+ documents  
+✓ **Free access**: No account or subscription required  
+✓ **Citation tracking**: "Cited by" for impact analysis  
+✓ **Multiple formats**: Articles, books, theses, patents  
+✓ **Full-text search**: Not just abstracts  
+
+Key strategies:
+- Use advanced operators for precision
+- Combine author, title, source searches
+- Track citations for impact
+- Export systematically to citation manager
+- Respect rate limits and access policies
+- Verify metadata with CrossRef/PubMed
+
+For biomedical research, complement with PubMed for MeSH terms and curated metadata.
+