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pubmed-verifier

Reference checker for AI-fabricated citations: batch-verify PMIDs against PubMed and catch the hallucination existence checks miss — a REAL PMID pointing to a DIFFERENT paper. Five-state citation verification (correct / mismatch / partial / invalid / unknown), citation-context parsing, Crossref DOI cross-check, retraction detection (capped at partial), correct-PMID suggestion, arXiv ID verification, plain-text reference list parsing, formatted reference lists (GB/T 7714 / Vancouver / APA / AMA), OpenAlex DOI fallback for non-Crossref registries, Chinese-reference title search, CSV/JSON claims, HTML/JSON/text reports. Four data sources: NCBI, Europe PMC fallback, Crossref, OpenAlex. Network failures are honestly reported as unverified, never as "not found". Zero dependencies, runs fully local. Triggers: verify PMIDs, check citations, citation audit, reference check, PMID check, batch verify references, AI hallucination detection, verify DOI, DOI check, citation formatting, reference formatter, GB/T 7714.

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Downloads

2.0k

Updated

Oct 9, 2026

Version

4.1.0

Source

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About

What it does, and when to use it.

Capability contract not published. No trust telemetry is available yet. 2K downloads reported by the source. Last updated 10/9/2026.

Avoid when

Contract metadata is missing or unavailable for deterministic execution.

Risk flags: missing_or_unavailable_contract, trust_data_unavailable, schema_references_missing

Public facts

Every fact links back to the source it came from.

Vendor: Clawhubvendor · observed Oct 9, 2026
Protocol compatibility: OpenClawcompatibility · observed Oct 9, 2026
Adoption signal: 2K downloadsadoption · observed Oct 9, 2026
Latest release: 4.1.0release · observed Oct 9, 2026
Handshake status: UNKNOWNsecurity

Install and run

Setup complexity: low.

clawhub skill install s17dagtwyk21qs6vpz98bzcrh1853t29:pubmed-verifier

Install using `clawhub skill install s17dagtwyk21qs6vpz98bzcrh1853t29:pubmed-verifier` in an isolated environment before connecting it to live workloads.
No published capability contract is available yet, so validate auth and request/response behavior manually.
Review the upstream CLAWHUB listing at https://clawhub.ai/docsor1212/pubmed-verifier before using production credentials.

Contract: missing

curl -s "https://www.xpersona.co/api/v1/agents/clawhub-docsor1212-pubmed-verifier/snapshot"

Documentation

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155,671 characters of source documentation, loaded on request.

Extracted files

5 files captured from the source.

SKILL.md

---
name: pubmed-verifier
license: MIT-0
version: 4.1.0
description: >-
  Reference checker for AI-fabricated citations: batch-verify PMIDs against
  PubMed and catch the hallucination existence checks miss — a REAL PMID
  pointing to a DIFFERENT paper. Five-state citation verification (correct /
  mismatch / partial / invalid / unknown), citation-context parsing, Crossref
  DOI cross-check, retraction detection (capped at partial), correct-PMID
  suggestion, arXiv ID verification, plain-text reference list parsing,
  formatted reference lists (GB/T 7714 / Vancouver / APA / AMA), OpenAlex DOI
  fallback for non-Crossref registries, Chinese-reference title search,
  CSV/JSON claims, HTML/JSON/text reports. Four data sources: NCBI, Europe PMC
  fallback, Crossref, OpenAlex. Network failures are honestly reported as
  unverified, never as "not found". Zero dependencies, runs fully local.
  Triggers: verify PMIDs, check citations, citation audit, reference check,
  PMID check, batch verify references, AI hallucination detection, verify DOI,
  DOI check, citation formatting, reference formatter, GB/T 7714.
---

# PubMed Citation Verifier v4.1.0

Batch verification of PMID citations via the PubMed E-utilities API. Not just
"does this PMID exist" — **does this PMID point to the paper you claim?**
Zero dependencies, pure standard library, fully local.

## When to use this skill

Invoke it whenever citation truth matters:

- "Verify / check these PMIDs / this reference list" (before submission or release)
- Auditing citations in AI-generated text (fabricated or mismatched references)
- Spot-checking a systematic review's bibliography
- "Does PMID 12345678 really say X?" — point-of-doubt verification
- Batch QA of a knowledge base's PMID/DOI citations
- Automatic invocation: trigger this skill whenever the user asks to
  "verify/check/audit" citations, PMIDs, DOIs, arXiv preprints or
  references — no flags needed for a first pass; add `--claims-file`
  when they supply the expected titles.

**Trigger priority & tool choice** — explicit "verify / check / audit
citations, references, PMIDs, DOIs" requests invoke this skill first.
cite-holmes is for deep research with machine-verified citations; when a
request mixes research and verification, run the research first, then
this tool for the final reference audit.

## The five-state verdict

| Verdict | Meaning |
|---------|---------|
| ✅ Correct | PMID exists AND matches the claimed paper |
| ⚠️ Mismatch | PMID exists but points to a **different** paper (the most common AI hallucination!) |
| 🔶 Partial | Some metadata matches (e.g. author+journal but title differs) |
| ❌ Invalid | PMID does not exist in PubMed |
| ❓ Unknown | Not enough claimed metadata to cross-check — or both data sources unreachable (never misreported as invalid) |

**Why existence checks are not enough:** a large share of fabricated
citations use REAL PMIDs that point to a different paper from the same
year/journal/field — in one of our o

examples/README.txt

claims.sample.csv — reference format for --claims-file

- pmid column: PubMed pipeline (full five-state verification)
- rows with only arxiv_id (+title): arXiv pipeline (official API check)
- doi column: DOI-splice cross-check against the PubMed-registered DOI
  (PMID rows) / version-of-record pairing check (arXiv rows, v3.3.0) /
  full five-state verdicts (doi-only rows, v3.4.0)
- title: required for verdicts beyond existence-check
- expected verdicts (as of v3.4.0): the 31018962 row carries a
  deliberately inexact title → partial (title mismatch, everything else
  matches — demonstrates the partial rung, not a data error); the
  1706.03762 row → correct; the doi-only 10.1371 row → correct (its
  second author "Other" is a synthetic placeholder; v3.8.0's
  mis-attribution cap means a wrong author set would drop it to partial); the 24476887 row
  (STAP cells) is RETRACTED on purpose → RETRACTED flag with a partial
  cap — it demonstrates retraction detection, not a data error

Run:  python3 scripts/verify_pmids.py --claims-file examples/claims.sample.csv

Lint first (offline, v3.5.0): python3 scripts/verify_pmids.py --lint-claims examples/claims.sample.csv

Bibliography (v3.6.0): refs.sample.bib audits a .bib file directly —
python3 scripts/verify_pmids.py --bibliography examples/refs.sample.bib

RIS (v3.7.0): refs.sample.ris audits Zotero/EndNote/Mendeley exports —
python3 scripts/verify_pmids.py --bibliography examples/refs.sample.ris

README.md

# PubMed Citation Verifier 🔬

[![GitHub Stars](https://img.shields.io/github/stars/docsor1212/pubmed-verifier?style=social&label=Star)](https://github.com/docsor1212/pubmed-verifier/stargazers)

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?

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

- **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

_meta.json

{
  "ownerId": "kn7b6sjwend7cwwmhf7mdg1wzx82dfbf",
  "slug": "pubmed-verifier",
  "version": "4.1.0",
  "publishedAt": 1791564939147
}

references/api_examples.md

# PubMed E-utilities API Quick Reference

## esummary — Article Metadata

```bash
# Single PMID
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=31018962&retmode=json"

# Batch (comma-separated)
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=31018962,22213727&retmode=json"
```

Response fields: `title`, `authors[].name`, `source` (journal), `pubdate`, `volume`, `pages`, `elocationid` (DOI).

Invalid PMID → `{"result": {"pmid": {"error": "cannot get document summary"}}}` (the exact string has varied over time — the verifier only checks for the presence of an `error` key).

## esearch — Find Articles by Query

```bash
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=Gattorno+classification+autoinflammatory&retmode=json&retmax=5"
```

Returns `esearchresult.idlist` → array of PMIDs.

## efetch — Full Abstracts

```bash
# efetch supports TEXT and XML only — retmode=json is NOT valid for efetch
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=37635643&rettype=abstract&retmode=text"
```

## Deep Research Workflow (Systematic PubMed Search)

When the user needs comprehensive medical literature research beyond simple PMID verification:

### Step 1: esearch → keyword search → get PMIDs
```bash
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=<keywords>&retmax=10&sort=relevance" | grep -oP '<Id>\K\d+'
```

### Step 2: esummary → metadata summaries (fast, compact)
```bash
PMIDS="pmid1,pmid2,pmid3"
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=$PMIDS&retmode=json" > /tmp/pubmed-results.json
python3 -c "
import json
data = json.load(open('/tmp/pubmed-results.json'))
for uid, art in data.get('result', {}).items():
    if uid == 'uids': continue
    authors = ', '.join([a.get('name','') for a in art.get('authors',[])[:6]])
    print(f'PMID {uid}: {art.get(\"title\",\"\")}')
    print(f'  {art.get(\"fulljournalname\",\"\")} {art.get(\"pubdate\",\"\")};{art.get(\"volume\",\"\")}:{art.get(\"pages\",\"\")}')
    print(f'  DOI: {art.get(\"elocationid\",\"\")}')
    print()
"
```

### Step 3: efetch → full abstracts for key papers
```bash
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$PMIDS&rettype=abstract&retmode=text"
```

### Pitfalls
- **efetch has no JSON mode** — use `retmode=text` (or XML) only
- **esearch may return unrelated results** — always cross-check with esummary titles
- **Rate limit**: 3 req/s without API key. Add `sleep 0.5` between batches
- **Large author lists**: esummary `authors` array can be 50+ — truncate to first 6 for display

## Rate Limits

- Without API key: 3 requests/second
- With API key (`&api_key=YOUR_KEY`): 10 requests/second
- API key obtained from NCBI Settings page
- Etiquette params: `&tool=pubmed-verifier&[email protected]` (added automatically with `--mailto`)

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