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# Citation Styles Reference
This document provides detailed guidelines for formatting citations in various academic styles commonly used in literature reviews.
## APA Style (7th Edition)
### Journal Articles
**Format**: Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. *Title of Periodical*, *volume*(issue), page range. https://doi.org/xx.xxx/yyyy
**Example**: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Machine learning approaches in drug discovery. *Nature Reviews Drug Discovery*, *22*(4), 301-318. https://doi.org/10.1038/nrd.2023.001
### Books
**Format**: Author, A. A. (Year). *Title of work: Capital letter also for subtitle*. Publisher Name. https://doi.org/xxxx
**Example**: Kumar, V., Abbas, A. K., & Aster, J. C. (2021). *Robbins and Cotran pathologic basis of disease* (10th ed.). Elsevier.
### Book Chapters
**Format**: Author, A. A., & Author, B. B. (Year). Title of chapter. In E. E. Editor & F. F. Editor (Eds.), *Title of book* (pp. xx-xx). Publisher.
**Example**: Brown, P. O., & Botstein, D. (2020). Exploring the new world of the genome with DNA microarrays. In M. B. Eisen & P. O. Brown (Eds.), *DNA microarrays: A molecular cloning manual* (pp. 1-45). Cold Spring Harbor Laboratory Press.
### Preprints
**Format**: Author, A. A., & Author, B. B. (Year). Title of preprint. *Repository Name*. https://doi.org/xxxx
**Example**: Zhang, Y., Chen, L., & Wang, H. (2024). Novel therapeutic targets in Alzheimer's disease. *bioRxiv*. https://doi.org/10.1101/2024.01.001
### Conference Papers
**Format**: Author, A. A. (Year, Month day-day). Title of paper. In E. E. Editor (Ed.), *Title of conference proceedings* (pp. xx-xx). Publisher. https://doi.org/xxxx
---
## Nature Style
### Journal Articles
**Format**: Author, A. A., Author, B. B. & Author, C. C. Title of article. *J. Name* **volume**, page range (year).
**Example**: Smith, J. D., Johnson, M. L. & Williams, K. R. Machine learning approaches in drug discovery. *Nat. Rev. Drug Discov.* **22**, 301-318 (2023).
### Books
**Format**: Author, A. A. & Author, B. B. *Book Title* (Publisher, Year).
**Example**: Kumar, V., Abbas, A. K. & Aster, J. C. *Robbins and Cotran Pathologic Basis of Disease* 10th edn (Elsevier, 2021).
### Multiple Authors
- 1-2 authors: List all
- 3+ authors: List first author followed by "et al."
**Example**: Zhang, Y. et al. Novel therapeutic targets in Alzheimer's disease. *bioRxiv* https://doi.org/10.1101/2024.01.001 (2024).
---
## Chicago Style (Author-Date)
### Journal Articles
**Format**: Author, First Name Middle Initial. Year. "Article Title." *Journal Title* volume, no. issue (Month): page range. https://doi.org/xxxx.
**Example**: Smith, John D., Mary L. Johnson, and Karen R. Williams. 2023. "Machine Learning Approaches in Drug Discovery." *Nature Reviews Drug Discovery* 22, no. 4 (April): 301-318. https://doi.org/10.1038/nrd.2023.001.
### Books
**Format**: Author, First Name Middle Initial. Year. *Book Title: Subtitle*. Edition. Place: Publisher.
**Example**: Kumar, Vinay, Abul K. Abbas, and Jon C. Aster. 2021. *Robbins and Cotran Pathologic Basis of Disease*. 10th ed. Philadelphia: Elsevier.
---
## Vancouver Style (Numbered)
### Journal Articles
**Format**: Author AA, Author BB, Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):page range.
**Example**: Smith JD, Johnson ML, Williams KR. Machine learning approaches in drug discovery. Nat Rev Drug Discov. 2023;22(4):301-18.
### Books
**Format**: Author AA, Author BB. Title of book. Edition. Place: Publisher; Year.
**Example**: Kumar V, Abbas AK, Aster JC. Robbins and Cotran pathologic basis of disease. 10th ed. Philadelphia: Elsevier; 2021.
### Citation in Text
Use superscript numbers in order of appearance: "Recent studies^1,2^ have shown..."
---
## IEEE Style
### Journal Articles
**Format**: [#] A. A. Author, B. B. Author, and C. C. Author, "Title of article," *Abbreviated Journal Name*, vol. x, no. x, pp. xxx-xxx, Month Year.
**Example**: [1] J. D. Smith, M. L. Johnson, and K. R. Williams, "Machine learning approaches in drug discovery," *Nat. Rev. Drug Discov.*, vol. 22, no. 4, pp. 301-318, Apr. 2023.
### Books
**Format**: [#] A. A. Author, *Title of Book*, xth ed. City, State: Publisher, Year.
**Example**: [2] V. Kumar, A. K. Abbas, and J. C. Aster, *Robbins and Cotran Pathologic Basis of Disease*, 10th ed. Philadelphia, PA: Elsevier, 2021.
---
## Common Abbreviations for Journal Names
- Nature: Nat.
- Science: Science
- Cell: Cell
- Nature Reviews Drug Discovery: Nat. Rev. Drug Discov.
- Journal of the American Chemical Society: J. Am. Chem. Soc.
- Proceedings of the National Academy of Sciences: Proc. Natl. Acad. Sci. U.S.A.
- PLOS ONE: PLoS ONE
- Bioinformatics: Bioinformatics
- Nucleic Acids Research: Nucleic Acids Res.
---
## DOI Best Practices
1. **Always verify DOIs**: Use the verify_citations.py script to check all DOIs
2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)
3. **No period after DOI**: DOI should be the last element without trailing punctuation
4. **Resolve redirects**: Check that DOIs resolve to the correct article
---
## In-Text Citation Guidelines
### APA Style
- (Smith et al., 2023)
- Smith et al. (2023) demonstrated...
- Multiple citations: (Brown, 2022; Smith et al., 2023; Zhang, 2024)
### Nature Style
- Superscript numbers: Recent studies^1,2^ have shown...
- Or: Recent studies (refs 1,2) have shown...
### Chicago Style
- (Smith, Johnson, and Williams 2023)
- Smith, Johnson, and Williams (2023) found...
---
## Reference List Organization
### By Citation Style
- **APA, Chicago**: Alphabetical by first author's last name
- **Nature, Vancouver, IEEE**: Numerical order of first appearance in text
### Hanging Indents
Most styles use hanging indents where the first line is flush left and subsequent lines are indented.
### Consistency
Maintain consistent formatting throughout:
- Capitalization (title case vs. sentence case)
- Journal name abbreviations
- DOI presentation
- Author name format

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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/