正文
获取原文件references/example_workflow.md
Illustrative end-to-end recipe, not an executed review. Run from the skill directory; populate the protocol, normalized search records, bibliography, and CSL file before the dependent commands. Dates below are a deliberately historical 2015-2024 interval.
Example Workflow
Complete workflow for a biomedical literature review:
# 1. Create review document from template
mkdir -p sources styles
cp assets/review_template.md crispr_sickle_cell_review.md
# 2. Optional supplementary discovery (authenticated Parallel account)
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 PubMed E-utilities and bioRxiv/medRxiv search or date-metadata APIs
# - Use direct API access for arXiv, Semantic Scholar
# - Save all pages and counts; document any API caps or failed requests
# - Normalize into a JSON array; keep raw exports and provenance
# 4. Process your normalized combined_results.json; raw API envelopes will fail
python scripts/search_databases.py combined_results.json \
--deduplicate \
--year-start 2015 \
--year-end 2024 \
--format markdown \
--output search_results.md \
--summary
# 5. Screen results and extract data
# - Request extracts with --full-content; obtain original reports and record failures
# - Use independent final full-text decisions and retain exclusion reasons
# - Track records, reports, studies, and overlapping participants separately
# - 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. Check DOI registration/metadata, then manually verify identity and claim support
python scripts/verify_citations.py crispr_sickle_cell_review.md
# Review the citation report
cat crispr_sickle_cell_review_citation_report.json
# Investigate missing/inconclusive results; transient failures do not invalidate citations
python scripts/verify_citations.py crispr_sickle_cell_review.md
# 8. Render after supplying bibliography, local CSL, and [@key] citations
# For manually typed references, omit those options; text will not be restyled
python scripts/generate_pdf.py crispr_sickle_cell_review.md \
--bibliography crispr_sickle_cell_review.bib --csl styles/nature.csl \
--output crispr_sickle_cell_review.pdf
# 9. Review final PDF and markdown outputs