PubMed Research

Use the bundled Python client for deterministic PubMed, PMC, Europe PMC, Unpaywall, MeSH, citation, and identifier tasks. It replaces the original TypeScript MCP server workflow with a skill-first workflow.

Configuration

Start from config.example.yaml. Keep real secrets out of the skill folder unless the user explicitly wants a local config file.

Preferred runtime configuration order:

1. Pass --config /path/to/config.yaml to scripts/pubmed.py.
2. Or set environment variables: NCBI_API_KEY, NCBI_ADMIN_EMAIL, UNPAYWALL_EMAIL, EUROPEPMC_EMAIL.
3. If neither is present, NCBI still works anonymously at the lower rate limit.

The API key placeholder is NCBI_API_KEY: "<YOUR_NCBI_API_KEY>" in config.example.yaml. Do not replace it with a real key unless the user provides one and asks you to write it.

Quick Commands

From this skill directory:

python3 scripts/pubmed.py search --query 'CRISPR cancer immunotherapy' --max-results 10 --summary-count 5 --format markdown
python3 scripts/pubmed.py fetch --pmids 31452104 38392781 --format json
python3 scripts/pubmed.py fulltext --pmcids PMC3531190 --sections methods results --format markdown
python3 scripts/pubmed.py cite --pmids 23193287 --style apa bibtex --format markdown
python3 scripts/pubmed.py related --pmid 23193287 --relationship similar --max-results 10
python3 scripts/pubmed.py spell --query 'brast canser'
python3 scripts/pubmed.py mesh --query 'myocardial infarction'
python3 scripts/pubmed.py lookup-citation --citation '{"journal":"proc natl acad sci u s a","year":"1991","volume":"88","firstPage":"3248","authorName":"mann bj"}'
python3 scripts/pubmed.py convert --id-type pmid --ids 23193287
python3 scripts/pubmed.py europepmc-search --query 'TITLE:"single cell" AND PUB_YEAR:2024' --page-size 10
python3 scripts/pubmed.py database-info

The default output is JSON. Use --format markdown when showing results to a user.

Workflow

1. For discovery, run search with --summary-count so the user gets titles and journals, not just PMIDs.
2. For known PMIDs, run fetch to retrieve structured metadata, abstracts, authors, DOI, PMCID, MeSH, keywords, and publication types.
3. For full text, prefer fulltext --pmcids when a PMCID is known. Use --pmids or --dois to let the script resolve through PMC, Europe PMC, and optionally Unpaywall.
4. For precise query expansion, run mesh and then search with quoted MeSH terms.
5. For noisy references, use lookup-citation before broad search.
6. For DOI/PMID/PMCID crosswalks, use convert; remember the PMC ID Converter only resolves records indexed in PMC.

Notes

• NCBI asks clients to send a tool name and contact email. Configure NCBI_ADMIN_EMAIL when possible.
• NCBI_API_KEY raises the NCBI rate ceiling. The script automatically uses a shorter delay when a key is present.
• UNPAYWALL_EMAIL enables legal open-access DOI fallback for full text when PMC/Europe PMC do not provide JATS XML.
• Europe PMC is enabled by default. Disable it in config with europepmc_enabled: false or env EUROPEPMC_ENABLED=false.
• Avoid logging or echoing full URLs that contain API keys. The script redacts api_key in error messages.