Synthesizing

Generate PRISMA flowcharts and synthesis reports for systematic literature review.

Overview

Generate final synthesis including PRISMA flowchart, included/excluded paper tables, and export options.

Prerequisite: Screening must be complete (scimesh:screening). Optionally, extraction too (scimesh:extracting).

Generate Stats from Vault

bash

# Screening statistics
uvx scimesh vault stats {review_path}/

Output:

code

Total papers: 120

  included:    31 (25.8%)
  excluded:    85 (70.8%)
  maybe:        4 (3.3%)
  unscreened:   0 (0.0%)

Progress: 100%

Generate PRISMA Flowchart

bash

# Generate PRISMA synthesis with mermaid flowchart and tables
uvx scimesh vault prisma {review_path}/ -o {review_path}/synthesis.md

This generates a complete synthesis document with:

•Mermaid PRISMA flowchart
•Summary statistics
•Included papers table
•Excluded papers table with reasons
•Protocol summary

Export Options

bash

# Export included papers to BibTeX
uvx scimesh vault export {review_path}/ --status included -f bibtex -o included.bib

# Export to RIS
uvx scimesh vault export {review_path}/ --status included -f ris -o included.ris

# Export to CSV (spreadsheet-friendly)
uvx scimesh vault export {review_path}/ -f csv -o all_papers.csv

# Export to JSON
uvx scimesh vault export {review_path}/ --status included -f json -o included.json

# Export to YAML
uvx scimesh vault export {review_path}/ -f yaml -o papers.yaml

Vault CLI Reference

bash

# Screening statistics
uvx scimesh vault stats {review_path}/

# List papers (table format)
uvx scimesh vault list {review_path}/

# List unscreened papers
uvx scimesh vault list {review_path}/ --status unscreened

# List included papers as paths
uvx scimesh vault list {review_path}/ --status included --format paths

# List papers as JSON
uvx scimesh vault list {review_path}/ --format json

# Generate PRISMA synthesis
uvx scimesh vault prisma {review_path}/ -o synthesis.md

Final Output Structure

code

{review_path}/
├── index.yaml          # Protocol + stats
├── searches.yaml       # Search history
├── papers.yaml         # Paper list with search_ids
├── synthesis.md        # PRISMA + synthesis (generated)
├── included.bib        # BibTeX of included papers
└── papers/
    └── {year}/             # Organized by publication year
        └── {paper-slug}/
            ├── index.yaml
            ├── fulltext.pdf
            ├── problem.md
            ├── method.md
            ├── result.md
            └── condensed.md

Ask Before Export Format

python

{
    "question": "How do you want to export the review?",
    "header": "Export",
    "options": [
        {"label": "Full synthesis (Rec)", "description": "PRISMA + tables + narrative"},
        {"label": "BibTeX only", "description": "Export citations for reference manager"},
        {"label": "CSV summary", "description": "Spreadsheet-friendly format"}
    ],
    "multiSelect": True
}