PubMed Citation Verifier 🔬

Batch-verify PMID citations against PubMed API. Built for researchers, medical writers, and evidence-based medicine teams.

简介（中文）

PubMed 文献引用批量验证工具——把引用列表交给它，逐条核验 PMID/DOI/arXiv ID 是否真实存在、是否指向你声称的那篇论文（AI 幻觉引用最常见的形态就是「真 PMID 指向别的论文」）。五态判定（正确/不匹配/部分匹配/无效/待确认），撤稿检测全覆盖，网络故障如实标注「未判定」、绝不误报「不存在」。零依赖、纯本地运行。

• 中文文献：GB/T 7714 格式参考文献可解析（……标题[J]. 刊名, 年… PMID: xxx）；--parse-text 粘贴即核验整张文献表——行内 PMID/DOI 精确路由，中文条目经 OpenAlex 标题检索判定（无编号 ID 也能核）
• 参考文献格式化：--format-references --citation-style gbt（另支持 Vancouver/APA/AMA），先验证后排版，只排已验真的条目
• 四数据源：NCBI PubMed、Europe PMC 自动兜底、Crossref、OpenAlex（DataCite/Zenodo 等非 Crossref 注册的 DOI 也可判定）
• 投稿就绪判定 + 审计底稿：每份报告自带证据链，--export-audit 输出可复放的 JSON 工作底稿

Why?

为什么要核验引用（中文）：学术项目的参考文献动辄数百条，人工核对既繁琐又易漏。在我们自己一次 225 条参考文献的审计中，发现了 3 个无效 PMID 和 6 条跨领域错配——任何一条混进稿件都足以动摇整项工作。AI 生成内容的高频问题是「真 PMID 指向别的论文」，存在性检查根本查不出来。

Academic projects routinely contain hundreds of PMID citations. Manual verification is tedious and error-prone. During our own 225-reference audit, we found 3 invalid PMIDs and 6 cross-domain mismatches — errors that would have undermined the entire project.

Features

核心能力（中文速览）：五态判定（正确/不匹配/部分匹配/无效/待确认）· 撤稿检测全覆盖+撤稿替代推荐 · DOI/arXiv/PMID 三类一站审计 · OpenAlex 兜底（DataCite/Zenodo DOI 可判定）· 中文文献 OpenAlex 标题检索 · 参考文献格式化导出（GB/T 7714/Vancouver/APA/AMA）· 差分审计（PRISMA 复跑只看变化）· 审计底稿可复放 · 网络故障诚实标注绝不误报不存在

• Batch verification — Scan entire project directories, extract all PMIDs, verify against PubMed in one run
• Mismatch detection — Five-state verdicts catch a REAL PMID pointing to a DIFFERENT paper (the most common AI hallucination)
• Metadata validation — Title, authors, journal and date fuzzy-compared against your claims (DOI cross-checked via Crossref with --verify-doi)
• Dual sources — NCBI E-utilities primary, Europe PMC automatic fallback when NCBI is unreachable
• Network hardening — Optional NCBI API key (3x faster batches), Crossref polite pool, 429 Retry-After backoff, UA rotation, per-host circuit breaker
• Content matching — Keyword overlap scoring flags potentially irrelevant citations
• Three citation types in one audit — PMIDs, DOIs and arXiv IDs (preprints) verified in a single scan; arXiv IDs checked against the official API (nonexistent = fabrication signal); claims rows keyed by DOI get full verdicts, and preprints surface their published version of record
• Claims lint — --lint-claims file.csv validates a claims file offline (ID shapes, missing titles, unknown columns, duplicates) before any verification run
• Bibliography audit — --bibliography refs.bib / refs.ris verifies BibTeX and RIS files directly (Zotero/EndNote/Mendeley exports; entries route by PMID > DOI > arXiv with full cross-checks); round-trips with --export-bibtex / --export-ris
• Plain-text reference list parsing — --parse-text refs.txt verifies a reference list copied straight out of a manuscript draft: numbered entries ([1], 1.) split cleanly, inline PMID/DOI/arXiv IDs route exactly, and a title-only entry resolves via PubMed title search (honestly labeled resolved_by: title_search, never a mismatch source)
• Formatted reference list export — --format-references out.txt --citation-style gbt|vancouver|apa|ama renders verified entries as a ready-to-paste numbered list (GB/T 7714-2015, Vancouver, APA 7th, AMA 11th); partial entries go to a manual-review section, retracted ones are excluded with a warning — formatting that stands on registry-verified records
• Retraction detection for every citation — the registry publication type ("Retracted Publication") flags retracted papers with no DOI or extra flags needed; Crossref updated-by adds the retraction-notice DOI
• Verified-bibliography export — --export-bibtex writes correct entries as BibTeX, comments partial ones, excludes and counts the rest
• Submission-readiness verdict — every report leads with SUBMISSION READY / NOT SUBMISSION-READY and per-problem counts
• Audit working-paper — --export-audit writes a self-contained JSON trail (tool identity, redacted invocation, evidence chain, verdict trace) a third party can replay
• DOI-native verification — --dois verifies DOIs directly (Crossref resolve, 404 = fabrication signal on explicit input); --source scans auto-extract DOIs; linked back to PMIDs via Europe PMC
• Delta audits — --diff previous-audit.json reports newly retracted, degraded, improved, new and dropped citations
• Exports — --export-audit (self-contained JSON trail), --export-bibtex (verified bibliography), --export-csv (spreadsheet audit table)
• Replacement search — Find correct PMIDs for broken citations via PubMed search
• Multiple output formats — HTML report, JSON (with per-entry metadata origin), or terminal summary

Quick Start

# Install
openclaw skills install docsor1212/pubmed-verifier

# 中文场景速览
python3 scripts/verify_pmids.py --parse-text references.txt --no-cache          # 核验整张参考文献表
python3 scripts/verify_pmids.py --parse-text references.txt --format-references out.txt --citation-style gbt
python3 scripts/verify_pmids.py --pmids 31018962,22213727                       # 批量验证 PMID
python3 scripts/verify_pmids.py --check-net                                     # 网络预检（五源）

# Verify all PMIDs in a project
python3 scripts/verify_pmids.py --source /path/to/project --output report.html

# Verify specific PMIDs
python3 scripts/verify_pmids.py --pmids 31018962,22213727,999999999

# Verify a reference list copied from a paper draft
python3 scripts/verify_pmids.py --parse-text references.txt --no-cache

# Format verified entries as a citation list (gbt | vancouver | apa | ama)
python3 scripts/verify_pmids.py --parse-text references.txt --format-references refs_gbt.txt --citation-style gbt

# Institutional mode: API key + polite pool
python3 scripts/verify_pmids.py --source ./papers --verify-doi --ncbi-api-key $NCBI_API_KEY --mailto you@lab.org

China mirror (ModelScope 魔搭): https://modelscope.cn/skills/Docsor/pubmed-verifier — if you find this skill useful, a like there helps others find it.

Use Cases

Scenario	Example
Systematic review QA	Verify all 200+ references before submission
Medical website audit	Check evidence citations across clinical case library
Paper manuscript check	Validate every PMID in your draft
Teaching material review	Ensure lecture citations are accurate
Evidence library maintenance	Periodic batch verification of reference databases
Draft reference list check & formatting	Paste a manuscript's reference list, verify it, get a GB/T 7714 / APA list back

Real-World Results

Audited a 35-file pediatric rheumatology evidence library (225 PMID citations):

• 222 citations: valid and content-matched ✅
• 3 citations: invalid PMIDs found and corrected
• 6 cross-domain citations: correctly flagged, reviewed, confirmed appropriate
• Total time: ~5 minutes for full audit

Technical Details

• APIs: PubMed E-utilities (esummary, esearch); Europe PMC fallback; Crossref DOI check
• Rate limit: 3 req/s free (0.4s batch delay), 10 req/s with --ncbi-api-key (0.12s)
• Resilience: 429 Retry-After backoff, 403/406 UA rotation, per-host circuit breaker
• Batch size: 50 PMIDs per request
• File types: .html, .md, .txt, .json, .htm
• PMID patterns: PMID: 12345678, PubMed: 12345678, pubmed.ncbi.nlm.nih.gov/12345678/
• Exit codes: 0 clean / 1 problems found / 2 network-incomplete

License

MIT-0