scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/.claude/skills/literature-review/references/database_strategies.md

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+# Literature Database Search Strategies
+
+This document provides comprehensive guidance for searching multiple literature databases systematically and effectively.
+
+## Available Databases and Skills
+
+### Biomedical & Life Sciences
+
+#### PubMed / PubMed Central
+- **Access**: Use `gget` skill or WebFetch tool
+- **Coverage**: 35M+ citations in biomedical literature
+- **Best for**: Clinical studies, biomedical research, genetics, molecular biology
+- **Search tips**: Use MeSH terms, Boolean operators (AND, OR, NOT), field tags [Title], [Author]
+- **Example**: `"CRISPR"[Title] AND "gene editing"[Title/Abstract] AND 2020:2024[Publication Date]`
+
+#### bioRxiv / medRxiv
+- **Access**: Use `gget` skill or direct API
+- **Coverage**: Preprints in biology and medicine
+- **Best for**: Latest unpublished research, cutting-edge findings
+- **Note**: Not peer-reviewed; verify findings with caution
+- **Search tips**: Search by category (bioinformatics, genomics, etc.)
+
+### General Scientific Literature
+
+#### arXiv
+- **Access**: Direct API access
+- **Coverage**: Preprints in physics, mathematics, computer science, quantitative biology
+- **Best for**: Computational methods, bioinformatics algorithms, theoretical work
+- **Categories**: q-bio (Quantitative Biology), cs.LG (Machine Learning), stat.ML (Statistics)
+- **Search format**: `cat:q-bio.QM AND title:"single cell"`
+
+#### Semantic Scholar
+- **Access**: Direct API (requires API key)
+- **Coverage**: 200M+ papers across all fields
+- **Best for**: Cross-disciplinary searches, citation graphs, paper recommendations
+- **Features**: Influential citations, paper summaries, related papers
+- **Rate limits**: 100 requests/5 minutes with API key
+
+#### Google Scholar
+- **Access**: Web scraping (use cautiously) or manual search
+- **Coverage**: Comprehensive across all fields
+- **Best for**: Finding highly cited papers, conference proceedings, theses
+- **Limitations**: No official API, rate limiting
+- **Export**: Use "Cite" feature for formatted citations
+
+### Specialized Databases
+
+#### ChEMBL / PubChem
+- **Access**: Use `gget` skill or `bioservices` skill
+- **Coverage**: Chemical compounds, bioactivity data, drug molecules
+- **Best for**: Drug discovery, chemical biology, medicinal chemistry
+- **ChEMBL**: 2M+ compounds, bioactivity data
+- **PubChem**: 110M+ compounds, assay data
+
+#### UniProt
+- **Access**: Use `gget` skill or `bioservices` skill
+- **Coverage**: Protein sequence and functional information
+- **Best for**: Protein research, sequence analysis, functional annotations
+- **Search by**: Protein name, gene name, organism, function
+
+#### KEGG (Kyoto Encyclopedia of Genes and Genomes)
+- **Access**: Use `bioservices` skill
+- **Coverage**: Pathways, diseases, drugs, genes
+- **Best for**: Pathway analysis, systems biology, metabolic research
+
+#### COSMIC (Catalogue of Somatic Mutations in Cancer)
+- **Access**: Use `gget` skill or direct download
+- **Coverage**: Cancer genomics, somatic mutations
+- **Best for**: Cancer research, mutation analysis
+
+#### AlphaFold Database
+- **Access**: Use `gget` skill with `alphafold` command
+- **Coverage**: 200M+ protein structure predictions
+- **Best for**: Structural biology, protein modeling
+
+#### PDB (Protein Data Bank)
+- **Access**: Use `gget` or direct API
+- **Coverage**: Experimental 3D structures of proteins, nucleic acids
+- **Best for**: Structural biology, drug design, molecular modeling
+
+### Citation & Reference Management
+
+#### OpenAlex
+- **Access**: Direct API (free, no key required)
+- **Coverage**: 250M+ works, comprehensive metadata
+- **Best for**: Citation analysis, author disambiguation, institutional research
+- **Features**: Open access, excellent for bibliometrics
+
+#### Dimensions
+- **Access**: Free tier available
+- **Coverage**: Publications, grants, patents, clinical trials
+- **Best for**: Research impact, funding analysis, translational research
+
+---
+
+## Search Strategy Framework
+
+### 1. Define Research Question (PICO Framework)
+
+For clinical/biomedical reviews:
+- **P**opulation: Who is the study about?
+- **I**ntervention: What is being tested?
+- **C**omparison: What is it compared to?
+- **O**utcome: What are the results?
+
+**Example**: "What is the efficacy of CRISPR-Cas9 gene therapy (I) for treating sickle cell disease (P) compared to standard care (C) in improving patient outcomes (O)?"
+
+### 2. Develop Search Terms
+
+#### Primary Concepts
+Identify 2-4 main concepts from your research question.
+
+**Example**:
+- Concept 1: CRISPR, Cas9, gene editing
+- Concept 2: sickle cell disease, SCD, hemoglobin disorders
+- Concept 3: gene therapy, therapeutic editing
+
+#### Synonyms & Related Terms
+List alternative terms, abbreviations, and related concepts.
+
+**Tool**: Use MeSH (Medical Subject Headings) browser for standardized terms
+
+#### Boolean Operators
+- **AND**: Narrows search (must include both terms)
+- **OR**: Broadens search (includes either term)
+- **NOT**: Excludes terms
+
+**Example**: `(CRISPR OR Cas9 OR "gene editing") AND ("sickle cell" OR SCD) AND therapy`
+
+#### Wildcards & Truncation
+- `*` or `%`: Matches any characters
+- `?`: Matches single character
+
+**Example**: `genom*` matches genomic, genomics, genome
+
+### 3. Set Inclusion/Exclusion Criteria
+
+#### Inclusion Criteria
+- **Date range**: e.g., 2015-2024 (last 10 years)
+- **Language**: English (or specify multilingual)
+- **Publication type**: Peer-reviewed articles, reviews, preprints
+- **Study design**: RCTs, cohort studies, meta-analyses
+- **Population**: Human, animal models, in vitro
+
+#### Exclusion Criteria
+- Case reports (n<5)
+- Conference abstracts without full text
+- Non-original research (editorials, commentaries)
+- Duplicate publications
+- Retracted articles
+
+### 4. Database Selection Strategy
+
+#### Multi-Database Approach
+Search at least 3 complementary databases:
+
+1. **Primary database**: PubMed (biomedical) or arXiv (computational)
+2. **Preprint server**: bioRxiv/medRxiv or arXiv
+3. **Comprehensive database**: Semantic Scholar or Google Scholar
+4. **Specialized database**: ChEMBL, UniProt, or field-specific
+
+#### Database-Specific Syntax
+
+| Database | Field Tags | Example |
+|----------|-----------|---------|
+| PubMed | [Title], [Author], [MeSH] | "CRISPR"[Title] AND 2020:2024[DP] |
+| arXiv | ti:, au:, cat: | ti:"machine learning" AND cat:q-bio.QM |
+| Semantic Scholar | title:, author:, year: | title:"deep learning" year:2020-2024 |
+
+---
+
+## Search Execution Workflow
+
+### Phase 1: Pilot Search
+1. Run initial search with broad terms
+2. Review first 50 results for relevance
+3. Note common keywords and MeSH terms
+4. Refine search strategy
+
+### Phase 2: Comprehensive Search
+1. Execute refined searches across all selected databases
+2. Export results in standard format (RIS, BibTeX, JSON)
+3. Document search strings and date for each database
+4. Record number of results per database
+
+### Phase 3: Deduplication
+1. Import all results into a single file
+2. Use `search_databases.py --deduplicate` to remove duplicates
+3. Identify duplicates by DOI (primary) or title (fallback)
+4. Keep the version with most complete metadata
+
+### Phase 4: Screening
+1. **Title screening**: Review titles, exclude obviously irrelevant
+2. **Abstract screening**: Read abstracts, apply inclusion/exclusion criteria
+3. **Full-text screening**: Obtain and review full texts
+4. Document reasons for exclusion at each stage
+
+### Phase 5: Quality Assessment
+1. Assess study quality using appropriate tools:
+   - **RCTs**: Cochrane Risk of Bias tool
+   - **Observational**: Newcastle-Ottawa Scale
+   - **Systematic reviews**: AMSTAR 2
+2. Grade quality of evidence (high, moderate, low, very low)
+3. Consider excluding very low-quality studies
+
+---
+
+## Search Documentation Template
+
+### Required Documentation
+All searches must be documented for reproducibility:
+
+```markdown
+## Search Strategy
+
+### Database: PubMed
+- **Date searched**: 2024-10-25
+- **Date range**: 2015-01-01 to 2024-10-25
+- **Search string**:
+  ```
+  ("CRISPR"[Title] OR "Cas9"[Title] OR "gene editing"[Title/Abstract])
+  AND ("sickle cell disease"[MeSH] OR "SCD"[Title/Abstract])
+  AND ("gene therapy"[MeSH] OR "therapeutic editing"[Title/Abstract])
+  AND 2015:2024[Publication Date]
+  AND English[Language]
+  ```
+- **Results**: 247 articles
+- **After deduplication**: 189 articles
+
+### Database: bioRxiv
+- **Date searched**: 2024-10-25
+- **Date range**: 2015-01-01 to 2024-10-25
+- **Search string**: "CRISPR" AND "sickle cell" (in title/abstract)
+- **Results**: 34 preprints
+- **After deduplication**: 28 preprints
+
+### Total Unique Articles
+- **Combined results**: 217 unique articles
+- **After title screening**: 156 articles
+- **After abstract screening**: 89 articles
+- **After full-text screening**: 52 articles included in review
+```
+
+---
+
+## Advanced Search Techniques
+
+### Citation Chaining
+
+#### Forward Citation Search
+Find papers that cite a key paper:
+- Use Google Scholar "Cited by" feature
+- Use OpenAlex or Semantic Scholar APIs
+- Identifies newer research building on seminal work
+
+#### Backward Citation Search
+Review references in key papers:
+- Extract references from included papers
+- Search for highly cited references
+- Identifies foundational research
+
+### Snowball Sampling
+1. Start with 3-5 highly relevant papers
+2. Extract all their references
+3. Check which references are cited by multiple papers
+4. Review those high-overlap references
+5. Repeat for newly identified key papers
+
+### Author Search
+Follow prolific authors in the field:
+- Search by author name across databases
+- Check author profiles (ORCID, Google Scholar)
+- Review recent publications and preprints
+
+### Related Article Features
+Many databases suggest related articles:
+- PubMed "Similar articles"
+- Semantic Scholar "Recommended papers"
+- Use to discover papers missed by keyword search
+
+---
+
+## Quality Control Checklist
+
+### Before Searching
+- [ ] Research question clearly defined
+- [ ] PICO criteria established (if applicable)
+- [ ] Search terms and synonyms listed
+- [ ] Inclusion/exclusion criteria documented
+- [ ] Target databases selected (minimum 3)
+- [ ] Date range determined
+
+### During Searching
+- [ ] Search string tested and refined
+- [ ] Results exported with complete metadata
+- [ ] Search parameters documented
+- [ ] Number of results recorded per database
+- [ ] Search date recorded
+
+### After Searching
+- [ ] Duplicates removed
+- [ ] Screening protocol followed
+- [ ] Reasons for exclusion documented
+- [ ] Quality assessment completed
+- [ ] All citations verified with verify_citations.py
+- [ ] Search methodology documented in review
+
+---
+
+## Common Pitfalls to Avoid
+
+1. **Too narrow search**: Missing relevant papers
+   - Solution: Include synonyms, related terms, broader concepts
+
+2. **Too broad search**: Thousands of irrelevant results
+   - Solution: Add specific concepts with AND, use field tags
+
+3. **Single database**: Incomplete coverage
+   - Solution: Search minimum 3 complementary databases
+
+4. **Ignoring preprints**: Missing latest findings
+   - Solution: Include bioRxiv, medRxiv, or arXiv
+
+5. **No documentation**: Irreproducible search
+   - Solution: Document every search string, date, and result count
+
+6. **Manual deduplication**: Time-consuming and error-prone
+   - Solution: Use search_databases.py script
+
+7. **Unverified citations**: Broken DOIs, incorrect metadata
+   - Solution: Run verify_citations.py on final reference list
+
+8. **Publication bias**: Only including published positive results
+   - Solution: Search trial registries, contact authors for unpublished data
+
+---
+
+## Example Multi-Database Search Workflow
+
+```python
+# Example workflow using available skills
+
+# 1. Search PubMed via gget
+search_term = "CRISPR AND sickle cell disease"
+# Use gget search pubmed search_term
+
+# 2. Search bioRxiv
+# Use gget search biorxiv search_term
+
+# 3. Search arXiv for computational papers
+# Search arXiv with: cat:q-bio AND "CRISPR" AND "sickle cell"
+
+# 4. Search Semantic Scholar via API
+# Use semantic scholar API with search query
+
+# 5. Aggregate and deduplicate results
+# python search_databases.py combined_results.json --deduplicate --format markdown --output review_papers.md
+
+# 6. Verify all citations
+# python verify_citations.py review_papers.md
+
+# 7. Generate final PDF
+# python generate_pdf.py review_papers.md --citation-style nature
+```
+
+---
+
+## Resources
+
+### MeSH Browser
+https://meshb.nlm.nih.gov/search
+
+### Boolean Search Tutorial
+https://www.ncbi.nlm.nih.gov/books/NBK3827/
+
+### Citation Style Guides
+See references/citation_styles.md in this skill
+
+### PRISMA Guidelines
+Preferred Reporting Items for Systematic Reviews and Meta-Analyses:
+http://www.prisma-statement.org/

scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py

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+#!/usr/bin/env python3
+"""
+PDF Generation Script for Literature Reviews
+Converts markdown files to professionally formatted PDFs with proper styling.
+"""
+
+import subprocess
+import sys
+import os
+from pathlib import Path
+
+def generate_pdf(
+    markdown_file: str,
+    output_pdf: str = None,
+    citation_style: str = "apa",
+    template: str = None,
+    toc: bool = True,
+    number_sections: bool = True
+) -> bool:
+    """
+    Generate a PDF from a markdown file using pandoc.
+
+    Args:
+        markdown_file: Path to the markdown file
+        output_pdf: Path for output PDF (defaults to same name as markdown)
+        citation_style: Citation style (apa, nature, chicago, etc.)
+        template: Path to custom LaTeX template
+        toc: Include table of contents
+        number_sections: Number the sections
+
+    Returns:
+        True if successful, False otherwise
+    """
+
+    # Verify markdown file exists
+    if not os.path.exists(markdown_file):
+        print(f"Error: Markdown file not found: {markdown_file}")
+        return False
+
+    # Set default output path
+    if output_pdf is None:
+        output_pdf = Path(markdown_file).with_suffix('.pdf')
+
+    # Check if pandoc is installed
+    try:
+        subprocess.run(['pandoc', '--version'], capture_output=True, check=True)
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        print("Error: pandoc is not installed.")
+        print("Install with: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
+        return False
+
+    # Build pandoc command
+    cmd = [
+        'pandoc',
+        markdown_file,
+        '-o', str(output_pdf),
+        '--pdf-engine=xelatex',  # Better Unicode support
+        '-V', 'geometry:margin=1in',
+        '-V', 'fontsize=11pt',
+        '-V', 'colorlinks=true',
+        '-V', 'linkcolor=blue',
+        '-V', 'urlcolor=blue',
+        '-V', 'citecolor=blue',
+    ]
+
+    # Add table of contents
+    if toc:
+        cmd.extend(['--toc', '--toc-depth=3'])
+
+    # Add section numbering
+    if number_sections:
+        cmd.append('--number-sections')
+
+    # Add citation processing if bibliography exists
+    bib_file = Path(markdown_file).with_suffix('.bib')
+    if bib_file.exists():
+        cmd.extend([
+            '--citeproc',
+            '--bibliography', str(bib_file),
+            '--csl', f'{citation_style}.csl' if not citation_style.endswith('.csl') else citation_style
+        ])
+
+    # Add custom template if provided
+    if template and os.path.exists(template):
+        cmd.extend(['--template', template])
+
+    # Execute pandoc
+    try:
+        print(f"Generating PDF: {output_pdf}")
+        print(f"Command: {' '.join(cmd)}")
+        result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+        print(f"✓ PDF generated successfully: {output_pdf}")
+        return True
+    except subprocess.CalledProcessError as e:
+        print(f"Error generating PDF:")
+        print(f"STDOUT: {e.stdout}")
+        print(f"STDERR: {e.stderr}")
+        return False
+
+def check_dependencies():
+    """Check if required dependencies are installed."""
+    dependencies = {
+        'pandoc': 'pandoc --version',
+        'xelatex': 'xelatex --version'
+    }
+
+    missing = []
+    for name, cmd in dependencies.items():
+        try:
+            subprocess.run(cmd.split(), capture_output=True, check=True)
+            print(f"✓ {name} is installed")
+        except (subprocess.CalledProcessError, FileNotFoundError):
+            print(f"✗ {name} is NOT installed")
+            missing.append(name)
+
+    if missing:
+        print("\n" + "="*60)
+        print("Missing dependencies:")
+        for dep in missing:
+            if dep == 'pandoc':
+                print("  - pandoc: brew install pandoc (macOS) or apt-get install pandoc (Linux)")
+            elif dep == 'xelatex':
+                print("  - xelatex: brew install --cask mactex (macOS) or apt-get install texlive-xetex (Linux)")
+        return False
+
+    return True
+
+def main():
+    """Command-line interface."""
+    if len(sys.argv) < 2:
+        print("Usage: python generate_pdf.py <markdown_file> [output_pdf] [--citation-style STYLE]")
+        print("\nOptions:")
+        print("  --citation-style STYLE    Citation style (default: apa)")
+        print("  --no-toc                  Disable table of contents")
+        print("  --no-numbers              Disable section numbering")
+        print("  --check-deps              Check if dependencies are installed")
+        sys.exit(1)
+
+    # Check dependencies mode
+    if '--check-deps' in sys.argv:
+        check_dependencies()
+        sys.exit(0)
+
+    # Parse arguments
+    markdown_file = sys.argv[1]
+    output_pdf = sys.argv[2] if len(sys.argv) > 2 and not sys.argv[2].startswith('--') else None
+
+    citation_style = 'apa'
+    toc = True
+    number_sections = True
+
+    # Parse optional flags
+    if '--citation-style' in sys.argv:
+        idx = sys.argv.index('--citation-style')
+        if idx + 1 < len(sys.argv):
+            citation_style = sys.argv[idx + 1]
+
+    if '--no-toc' in sys.argv:
+        toc = False
+
+    if '--no-numbers' in sys.argv:
+        number_sections = False
+
+    # Generate PDF
+    success = generate_pdf(
+        markdown_file,
+        output_pdf,
+        citation_style=citation_style,
+        toc=toc,
+        number_sections=number_sections
+    )
+
+    sys.exit(0 if success else 1)
+
+if __name__ == "__main__":
+    main()