# 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:
```bash
# 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:
```bash
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- Preprints are not peer-reviewed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:
```python
# 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):
   - 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
     ```
   - Use Google Scholar "Cited by"
   - Use Semantic Scholar or OpenAlex APIs
   - Identifies newer research building on seminal work

2. **Backward citations** (references from key papers):
   - 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
     ```
   - Extract references from included papers
   - Identify highly cited foundational work
   - 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:

| Paper Age | Citation Threshold | Classification |
|-----------|-------------------|----------------|
| 0-3 years | 20+ citations | Noteworthy |
| 0-3 years | 100+ citations | Highly Influential |
| 3-7 years | 100+ citations | Significant |
| 3-7 years | 500+ citations | Landmark Paper |
| 7+ years | 500+ citations | Seminal Work |
| 7+ years | 1000+ citations | Foundational |

#### 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)