@synsci/cli-darwin-x64 1.1.97 → 1.1.99

package/bin/skills/literature-review/references/database_strategies.md

@@ -1,455 +0,0 @@
-# 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-- **Best for**: Latest unpublished research, cutting-edge findings
-- **Note**: Not peer-reviewed; verify findings with caution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
-
-### Prioritizing High-Impact Papers (CRITICAL)
-
-**Always prioritize papers based on citation count, venue quality, and author reputation.** Quality matters more than quantity.
-
-#### Citation Metrics in Database Searches
-
-Use citation counts to identify influential work:
-
-| Paper Age | Citations | Classification |
-|-----------|-----------|----------------|
-| 0-3 years | 20+ | Noteworthy |
-| 0-3 years | 100+ | Highly Influential |
-| 3-7 years | 100+ | Significant |
-| 3-7 years | 500+ | Landmark |
-| 7+ years | 500+ | Seminal |
-| 7+ years | 1000+ | Foundational |
-
-**Database-Specific Citation Features:**
-- **Google Scholar:** Sort by citation count, use "Cited by" feature
-- **Semantic Scholar:** "Highly Influential Citations" metric, citation velocity
-- **OpenAlex:** Citation counts, citation context analysis
-- **PubMed:** Use "Cited by" in PMC, check citation counts via Google Scholar
-
-#### Filtering by Journal Quality
-
-Prioritize papers from higher-tier venues:
-
-**Tier 1 (Always Prefer):**
-- Nature, Science, Cell, NEJM, Lancet, JAMA, PNAS
-- Nature Medicine, Nature Biotechnology, Nature Methods
-- Search tip: `source:Nature` or `journal:Nature` in Google Scholar
-
-**Tier 2 (High Priority):**
-- High-impact specialized journals (Impact Factor >10)
-- Top conferences: NeurIPS, ICML, ICLR, CVPR, ACL
-
-**Tier 3 (Include When Relevant):**
-- Respected field-specific journals (IF 5-10)
-
-**PubMed Journal Filtering:**
-```
-"Nature"[Journal] OR "Science"[Journal] OR "Cell"[Journal]
-```
-
-**Google Scholar Journal Filtering:**
-```
-source:Nature source:Science source:Cell
-```
-
-#### Leveraging "Cited by" Features
-
-**Finding Influential Work:**
-1. Start with a known key paper
-2. Click "Cited by" to find papers that cite it
-3. Sort citing papers by their citation count
-4. Highly-cited citing papers indicate important follow-up work
-
-**Identifying Seminal Papers:**
-1. Search your topic broadly
-2. Note which papers appear repeatedly in reference lists
-3. Papers cited by many of your results are likely seminal
-4. Check citation counts to confirm influence
-
-**Semantic Scholar Features:**
-- "Highly Influential Citations" shows citations that significantly built on the paper
-- "Citation Velocity" shows recent citation growth
-- Paper recommendations based on citation networks
-
-### 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
-- **Tip:** Sort by citation count to find the most influential follow-up work
-
-#### Backward Citation Search
-Review references in key papers:
-- Extract references from included papers
-- Search for highly cited references (500+ citations for older papers)
-- Identifies foundational research
-- **Tip:** Focus on references that appear in multiple papers' bibliographies
-
-### Snowball Sampling
-1. Start with 3-5 highly relevant papers **from Tier-1 venues**
-2. Extract all their references
-3. Check which references are cited by multiple papers
-4. Review those high-overlap references - these are likely seminal
-5. Repeat for newly identified key papers
-6. **Prioritize papers with high citation counts** at each step
-
-### Author Search
-Follow prolific and reputable authors in the field:
-- Search by author name across databases
-- Check author profiles (ORCID, Google Scholar) for h-index and publication venues
-- Review recent publications and preprints
-- **Prefer authors with multiple Tier-1 publications** and high h-index (>40)
-- Look for senior authors who are recognized field leaders
-
-### Related Article Features
-Many databases suggest related articles:
-- PubMed "Similar articles"
-- Semantic Scholar "Recommended papers"
-- Use to discover papers missed by keyword search
-- **Filter recommendations by citation count and venue quality**
-
----
-
-## 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/

package/bin/skills/literature-review/scripts/generate_pdf.py

@@ -1,184 +0,0 @@
-#!/usr/bin/env python3
-"""
-PDF Generation Script for Literature Reviews
-Converts markdown files to professionally formatted PDFs with proper styling.
-"""
-
-import os
-import subprocess
-import sys
-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("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()