Database Search Guidance and Citation Styles

Per-database search guidance (coverage, syntax, and export paths) followed by the citation style guide. See also database_strategies.md and citation_styles.md.

Database-Specific Search Guidance

PubMed / PubMed Central

Access via gget skill:

# Search PubMed
gget search pubmed "CRISPR gene editing" -l 100

# Search with filters
# Use PubMed Advanced Search Builder to construct complex queries
# Then execute via gget or direct Entrez API

Search tips: - Use MeSH terms: "sickle cell disease"[MeSH] - Field tags: [Title], [Title/Abstract], [Author] - Date filters: 2020:2024[Publication Date] - Boolean operators: AND, OR, NOT - See MeSH browser: https://meshb.nlm.nih.gov/search

bioRxiv / medRxiv

Access via gget skill:

gget search biorxiv "CRISPR sickle cell" -l 50

Important considerations: - Preprints are not peer-reviewed - Verify findings with caution - Check if preprint has been published (CrossRef) - Note preprint version and date

arXiv

Access via direct API or WebFetch:

# Example search categories:
# q-bio.QM (Quantitative Methods)
# q-bio.GN (Genomics)
# q-bio.MN (Molecular Networks)
# cs.LG (Machine Learning)
# stat.ML (Machine Learning Statistics)

# Search format: category AND terms
search_query = "cat:q-bio.QM AND ti:\"single cell sequencing\""

Semantic Scholar

Access via direct API (requires API key, or use free tier): - 200M+ papers across all fields - Excellent for cross-disciplinary searches - Provides citation graphs and paper recommendations - Use for finding highly influential papers

Specialized Biomedical Databases

Use appropriate skills: - ChEMBL: bioservices skill for chemical bioactivity - UniProt: gget or bioservices skill for protein information - KEGG: bioservices skill for pathways and genes - COSMIC: gget skill for cancer mutations - AlphaFold: gget alphafold for protein structures - PDB: gget or direct API for experimental structures

Citation Chaining

Expand search via citation networks:

1. Forward citations (papers citing key papers):
2. Use parallel-cli search to find papers citing a specific work: bash parallel-cli search "papers citing [Author et al. Year] [paper title]" \ -q "citing" -q "[key author]" \ --json --max-results 10 --excerpt-max-chars-total 27000 \ --include-domains "scholar.google.com,semanticscholar.org,arxiv.org,pubmed.ncbi.nlm.nih.gov" \ -o sources/litreview_forward_citations.json
3. Use Google Scholar "Cited by"
4. Use Semantic Scholar or OpenAlex APIs

5. Identifies newer research building on seminal work

6. Backward citations (references from key papers):

7. Use parallel-cli extract to fetch full text of key papers and extract their reference lists: bash parallel-cli extract "https://doi.org/10.xxxx/yyyy" --json
8. Extract references from included papers
9. Identify highly cited foundational work
10. Find papers cited by multiple included studies

Citation Style Guide

Detailed formatting guidelines are in references/citation_styles.md. Quick reference:

APA (7th Edition)

• In-text: (Smith et al., 2023)
• Reference: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title. Journal, 22(4), 301-318. https://doi.org/10.xxx/yyy

Nature

• In-text: Superscript numbers^1,2^
• Reference: Smith, J. D., Johnson, M. L. & Williams, K. R. Title. Nat. Rev. Drug Discov. 22, 301-318 (2023).

Vancouver

• In-text: Superscript numbers^1,2^
• Reference: Smith JD, Johnson ML, Williams KR. Title. Nat Rev Drug Discov. 2023;22(4):301-18.

Always verify citations with verify_citations.py before finalizing.

Prioritizing High-Impact Papers (CRITICAL)

Always prioritize influential, highly-cited papers from reputable authors and top venues. Quality matters more than quantity in literature reviews.

Citation Count Thresholds

Use citation counts to identify the most impactful papers:

Journal and Venue Tiers

Prioritize papers from higher-tier venues:

• Tier 1 (Always Prefer): Nature, Science, Cell, NEJM, Lancet, JAMA, PNAS, Nature Medicine, Nature Biotechnology
• Tier 2 (Strong Preference): High-impact specialized journals (IF>10), top conferences (NeurIPS, ICML for ML/AI)
• Tier 3 (Include When Relevant): Respected specialized journals (IF 5-10)
• Tier 4 (Use Sparingly): Lower-impact peer-reviewed venues

Author Reputation Assessment

Prefer papers from: - Senior researchers with high h-index (>40 in established fields) - Leading research groups at recognized institutions (Harvard, Stanford, MIT, Oxford, etc.) - Authors with multiple Tier-1 publications in the relevant field - Researchers with recognized expertise (awards, editorial positions, society fellows)

Identifying Seminal Papers

For any topic, identify foundational work by: 1. High citation count (typically 500+ for papers 5+ years old) 2. Frequently cited by other included studies (appears in many reference lists) 3. Published in Tier-1 venues (Nature, Science, Cell family) 4. Written by field pioneers (often cited as establishing concepts)