Biomedical Reference Verifier

Verify and normalize biomedical and life-science reference lists, with a focus on AI-caused citation errors.

The skill checks DOI, PMID, title, authors, journal, year, and other bibliographic metadata through Crossref, PubMed, and OpenAlex. It can also normalize references to AMA, APA, Vancouver, or GB/T 7714 style without overwriting the source document.

Highlights

• Fast, Balanced, and Strict verification modes
• DOI-first batch verification and early DOI recovery
• Crossref, PubMed, and OpenAlex evidence
• Bounded retries and PubMed batch-failure isolation
• Detection of identifier hijacking and shifted identifiers
• Reusable audit indexes with lossless audit/index conversion
• Tolerant handling of user-edited prior artifacts
• Runtime metrics and request-event logging
• No hidden persistent cache
• Severe references are reported, never automatically deleted

Requirements

• Python 3
• Standard library only
• Optional NCBI_API_KEY for higher PubMed limits
• Optional OPENALEX_API_KEY

Quick start

python3 scripts/verify_references.py refs.md --mode balanced --output-dir reference-audit

Format without external verification:

python3 scripts/verify_references.py refs.md --pipeline format-only --citation-style ama

Run the offline regression suite:

python3 scripts/self_test_verify_references.py

See SKILL.md for the complete workflow and verification_policy.md for classification and evidence rules.

License

MIT-0