Ma Search Bibliography

Ma Search Bibliography

Overview

Run reproducible database searches, capture the search strategy, and produce versioned .bib files.

Inputs

• 01_protocol/search-plan.md
• 01_protocol/pico.yaml

Outputs

• 02_search/round-01/queries.txt
• 02_search/round-01/results.bib
• 02_search/round-01/dedupe.bib
• 02_search/round-01/log.md

Workflow

1. Translate PICO terms into database-specific queries and save them in queries.txt.
   • Read from 01_protocol/pico.yaml (L1-8: population, intervention, comparison fields)
   • Write to 02_search/round-01/queries.txt
2. Initialize Python tooling with uv in tooling/python/ using uv init and uv add dependencies.
3. Run search scripts with uv run from tooling/python/ (avoid direct python3 calls).
   • Use scripts/pubmed_fetch.py (L105-155: fetch_pubmed_records function)
   • Use scripts/scopus_fetch.py for Scopus API
4. Use uv tool for any one-off CLI utilities (do not install them globally).
5. Always search PubMed + Scopus as the mandatory minimum (PRISMA requires ≥2 databases). Optionally extend to Embase and Cochrane if defined in the protocol.
6. Export results to .bib and record the run date, database, and query hash in log.md.
   • Use scripts/pubmed_fetch.py (L54-103: build_bib_entry function)
   • Write to 02_search/round-01/results.bib
   • Write metadata to 02_search/round-01/log.md
7. Deduplicate by DOI, PMID, and title, then save dedupe.bib.
   • Use scripts/dedupe_bib.py
   • Write to 02_search/round-01/dedupe.bib
8. If running updates, increment the round folder name and record deltas.
9. Generate PRISMA flowchart after search completion using generate_prisma_flowchart.R (see below).
   • Use scripts/generate_prisma_flowchart.R
   • Output: 02_search/prisma-flow.png (300 DPI minimum)

PubMed Implementation Notes

• Use scripts/pubmed_fetch.py for the default PubMed pipeline with uv run.
• Set an email and API key, respect rate limits, and use history for batch retrieval.
• See references/pubmed-eutils.md for a compact tutorial and API notes.
• Read API keys from .env in the project root.

Resources

Python Scripts (Search & Deduplication)

• scripts/pubmed_fetch.py fetches PubMed records and writes BibTeX.
• scripts/dedupe_bib.py removes duplicate records based on DOI, PMID, or title.
• scripts/build_queries.py builds multi-DB queries from pico.yaml.
• scripts/mesh_expand.py expands terms via the MeSH RDF lookup service.
• scripts/expand_terms.py expands PICO terms using MeSH and optional Emtree synonyms.
• scripts/run_multi_db_search.py runs multi-DB search, merge, and counts.
• scripts/multi_db_dedupe.py merges and deduplicates multiple BibTeX files.
• scripts/db_counts.py summarizes per-database counts for PRISMA.
• scripts/search_report.py generates a per-database query + count report.
• scripts/search_audit.py generates a JSON audit with query hashes and parameters.
• scripts/scopus_fetch.py fetches Scopus Search API results.
• scripts/embase_fetch.py fetches Embase Search API results.
• scripts/cochrane_fetch.py fetches Cochrane ReviewDB API results.
• scripts/bib_subset_by_ids.py extracts a BibTeX subset from CSV record IDs.
• scripts/zotero_fetch.py fetches records from a Zotero collection.
• scripts/zotero_sync.py syncs a .bib file back to a Zotero collection.
• scripts/env_utils.py loads .env credentials.

R Scripts (PRISMA Flowchart)

• scripts/generate_prisma_flowchart.R generates PRISMA 2020 compliant flow diagrams in PNG/PDF/SVG/HTML formats.

Reference Documentation

• references/pubmed-eutils.md summarizes the E-utilities workflow.
• references/database-auth.md summarizes authentication per database.
• references/emtree-synonyms-template.csv provides a template for Emtree synonyms.
• references/prisma-flowchart-guide.md provides complete PRISMA 2020 flowchart generation guide.

Notes

• Keep all rounds. Do not overwrite prior .bib files.
• Add a short note in each .bib entry for the round (example: note = {round-01} ).

PRISMA Flowchart Generation

Purpose: Generate publication-quality PRISMA 2020 flow diagrams automatically.

When: After completing database searches and deduplication.

Command:

cd ma-search-bibliography/scripts

Rscript generate_prisma_flowchart.R \
  DB_RECORDS \
  SCREENED \
  EXCLUDED \
  FULLTEXT \
  INCLUDED \
  [PARTICIPANTS] \
  [OUTPUT_DIR]

Example (after search completion, before screening):

# Count database records
DB_RECORDS=$(wc -l < ../../projects/<project-name>/02_search/round-01/dedupe.bib | xargs)

# Generate initial flowchart (screening numbers TBD)
Rscript generate_prisma_flowchart.R $DB_RECORDS 0 0 0 0 NA ../../projects/<project-name>/figures/

Outputs:

• prisma_flowchart.png (300 DPI, for manuscript)
• prisma_flowchart.pdf (vector, for publication)
• prisma_flowchart.svg (scalable, for presentations)
• prisma_flowchart_interactive.html (interactive, for supplementary materials)

Time: 30 seconds to 2 minutes

See: references/prisma-flowchart-guide.md for complete documentation

Validation

• Confirm query coverage matches the protocol scope.
• Verify dedupe retains the best metadata per record.
• Generate PRISMA flowchart to visualize search results and verify counts.

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