# Example Workflow

A complete worked review from scoping through generated document.

## Example Workflow

Complete workflow for a biomedical literature review:

```bash
# 1. Create review document from template
cp assets/review_template.md crispr_sickle_cell_review.md

# 2. Start with parallel-web for broad academic search
parallel-cli search "CRISPR Cas9 sickle cell disease gene therapy efficacy" \
  -q "CRISPR" -q "sickle cell" -q "gene therapy" \
  --json --max-results 10 --excerpt-max-chars-total 27000 \
  --include-domains "scholar.google.com,arxiv.org,pubmed.ncbi.nlm.nih.gov,semanticscholar.org,biorxiv.org,nature.com,science.org,cell.com,pnas.org,nih.gov" \
  -o sources/litreview_crispr_scd-academic.json

parallel-cli search "CRISPR sickle cell disease clinical trials treatment" \
  -q "CRISPR" -q "sickle cell" \
  --json --max-results 10 --excerpt-max-chars-total 27000 \
  -o sources/litreview_crispr_scd-general.json

# 3. Search specialized databases using appropriate skills
# - Use gget skill for PubMed, bioRxiv
# - Use direct API access for arXiv, Semantic Scholar
# - Export results in JSON format

# 4. Aggregate and process results (combine parallel-cli + database results)
python scripts/search_databases.py combined_results.json \
  --deduplicate \
  --rank citations \
  --year-start 2015 \
  --year-end 2024 \
  --format markdown \
  --output search_results.md \
  --summary

# 5. Screen results and extract data
# - Use parallel-cli extract to fetch full content from promising URLs
# - Manually screen titles, abstracts, full texts
# - Extract key data into the review document
# - Organize by themes

# 6. Write the review following template structure
# - Introduction with clear objectives
# - Detailed methodology section
# - Results organized thematically
# - Critical discussion
# - Clear conclusions

# 7. Verify all citations
python scripts/verify_citations.py crispr_sickle_cell_review.md

# Review the citation report
cat crispr_sickle_cell_review_citation_report.json

# Fix any failed citations and re-verify
python scripts/verify_citations.py crispr_sickle_cell_review.md

# 8. Generate professional PDF
python scripts/generate_pdf.py crispr_sickle_cell_review.md \
  --citation-style nature \
  --output crispr_sickle_cell_review.pdf

# 9. Review final PDF and markdown outputs
```