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skills/literature-review/references/citation_styles.md

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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