Medsci-skills verify-refs

Audit-only verification of manuscript references against PubMed and CrossRef. Detects fabricated or mismatched citations and writes qc/reference_audit.json. Does not modify references/ or refs.bib.

install

source · Clone the upstream repo

git clone https://github.com/Aperivue/medsci-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/Aperivue/medsci-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/verify-refs" ~/.claude/skills/aperivue-medsci-skills-verify-refs && rm -rf "$T"

manifest: skills/verify-refs/SKILL.md

source content

Verify References (Audit-Only)

You help a medical researcher prevent reference hallucinations before submission. This skill audits an existing manuscript or bibliography. It does not write to

references/

manuscript/_src/refs.bib

. It does not discover new literature; use

/search-lit

for discovery and

/lit-sync

for bib management.

When to Use

Before journal submission, especially for
```
.docx
```
manuscripts inherited from coauthors or external editors.
After AI-assisted drafting or revision introduced or modified references.
When a reviewer or collaborator flags a possibly fabricated citation.
Before
```
/sync-submission
```
freezes a journal package.

Inputs

Manuscript or bibliography path:
```
.md
```
,
```
.docx
```
,
```
.bib
```
,
```
.txt
```
, or
```
.tsv
```
.
Optional project root. Default: current working directory.
Optional flags passed to the script:
- ```
--offline
```
  : extract and classify references without API verification.
- ```
--timeout N
```
  : HTTP timeout seconds.

Deterministic Script

Run the bundled script rather than verifying citations by memory:

python "${CLAUDE_SKILL_DIR}/scripts/verify_refs.py" manuscript/manuscript.md --project-root .

For hooks or quick manual runs, use the wrapper:

"${CLAUDE_SKILL_DIR}/scripts/verify_cli.sh" manuscript/manuscript.md --offline

Manual pre-submission strict run (Phase 1A.5):

"${CLAUDE_SKILL_DIR}/scripts/verify_cli.sh" manuscript/index.qmd --strict

--strict

forbids

--offline

and exits non-zero on any UNVERIFIED row. Full checkpoint protocol:

references/manual_checkpoint_guide.md

The script uses DOI, PMID, CrossRef, and PubMed E-utilities where available. If network verification fails, it records

UNVERIFIED

rather than silently passing.

Output Contract (v1.1.1)

Artifact	Path	Purpose
Audit JSON	`qc/reference_audit.json`	Sole output — row-level status (OK/MISMATCH/UNVERIFIED/FABRICATED), counts, submission-safe flag, full records

Removed in Phase 1A.2 (per

docs/artifact_contract.md

references/verified_references.tsv

— record-level details now live inside

reference_audit.json

under

records[]

```
references/library.bib
```
— never this skill's concern.
```
/search-lit
```
produces candidates;
```
/lit-sync
```
(via Better BibTeX) writes
```
manuscript/_src/refs.bib
```
.

Sole-writer enforcement:

scripts/validate_project_contract.py

will flag any

references/*

file written by this skill as drift.

Workflow

Identify the input file and project root.
Run
```
scripts/verify_refs.py
```
.
Read
```
qc/reference_audit.json
```
.
Report all
```
FABRICATED
```
and
```
MISMATCH
```
rows first (from
```
records[]
```
).
If
```
UNVERIFIED
```
rows remain, list them as manual checks and do not call the manuscript fully submission-safe.
If the user needs a human-readable table, summarize from
```
records[]
```
in chat — do not write a TSV.

Quality Gates

Gate 1: stop submission if any row is
```
FABRICATED
```
.
Gate 2: require user confirmation before accepting
```
UNVERIFIED
```
references.
Gate 3: rerun after any reference edits.

What This Skill Does NOT Do

Does not generate new references from memory.
Does not replace missing citations with plausible alternatives without
```
/search-lit
```
or user approval.
Does not sync Zotero collections; use
```
/lit-sync
```
after this audit.

Anti-Hallucination

Never fabricate titles, DOIs, PMIDs, author lists, journal names, years, volumes, or pages.
Every OK row must be backed by DOI, PMID, CrossRef, or PubMed title evidence.
If evidence is unavailable, mark
```
UNVERIFIED
```
and keep it visible.