Agent skill

Validate Bib

by pedrohcgs in pedrohcgs/claude-code-my-workflow

Validate bibliography entries against citations in all lecture files.

MITAuto-check: notesResearch & Science

Install Validate Bib

skills CLI
$ npx skills add pedrohcgs/claude-code-my-workflow --skill validate-bib -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install pedrohcgs/claude-code-my-workflow validate-bib --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/pedrohcgs/claude-code-my-workflow.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/validate-bib .claude/skills/validate-bib && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
validate-bib
GitHub stars
1.6k
Token cost
~1.5k tokens
SKILL.md length
582 words
Files
1
Skills in repo
59
Repo updated
First seen
Licence
MIT

At a glance

Validate bibliography entries against citations in all lecture files.

  • Works in 5 steps: Read the bibliography file and extract… → Scan lecture files for citation keys → Cross-reference → …
  • Tasks that involve Citation management
  • SKILL.md covers Mode 1: Structural (default), Mode 2: Semantic (--semantic), Exit behavior and Cross-references, plus 1 more section
  • Reaches doi.org and api.crossref.org

What it does

Validate Bib is an agent skill from pedrohcgs/claude-code-my-workflow. Validate bibliography entries against citations in all lecture files. Structural checks (missing/unused entries, malformed fields) by default; --semantic adds citation-drift detection, DOI verification, and style-consistency checks.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Citation management and GitOps. The repository describes itself as: A ready-to-fork Claude Code template for academics using LaTeX/Beamer + R. Multi-agent review, quality gates, adversarial QA, and replication protocols. The licence is MIT.

When your agent uses it

  • Tasks that involve Citation management
  • Tasks that involve GitOps

Example prompts

  • “/validate-bib”

Requirements

  • Pre-approved tools (allowed-tools): Read, Grep, Glob, Write, Bash, WebFetch

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Read the bibliography file and extract all citation keys.
  2. Scan lecture files for citation keys
  3. Cross-reference
  4. Check entry quality
  5. Write report to quality_reports/bib_audit_structural.md.

What it can do on your machine

Read from SKILL.md and the folder at commit ae72617. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Grep
    • Glob
    • Write
    • Bash
    • WebFetch

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are markdown).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • doi.org
    • api.crossref.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Validate Bib loads about 1.5k tokens when it runs. Until then it costs about 62 tokens; SKILL.md has 582 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~62
When it runs · the whole SKILL.md, loaded when a task matches
~1.5k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Read, Grep, Glob, Write, Bash, WebFetch

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from pedrohcgs/claude-code-my-workflow at commit ae72617, republished under its MIT licence (© pedrohcgs). 582 words, ~1,544 tokens.

Download SKILL.mdSave it as .claude/skills/validate-bib/SKILL.md (or your agent's skills folder).
name
validate-bib
description
Validate bibliography entries against citations in all lecture files. Structural checks (missing/unused entries, malformed fields) by default; `--semantic` adds citation-drift detection, DOI verification, and style-consistency checks.
allowed-tools
Read, Grep, Glob, Write, Bash, WebFetch
argument-hint
[--semantic] [--skip-doi] [--cite-claim]

Validate Bibliography

Cross-reference citations in lecture files against bibliography entries. Two modes:

  • Default (structural): missing entries, unused entries, malformed fields, typo candidates.
  • --semantic: adds citation-drift detection (duplicate entries for the same paper), DOI verification via crossref, and citation-style consistency within each file.

Report saved to quality_reports/bib_audit_[structural|semantic].md.

Mode 1: Structural (default)

Steps
  1. Read the bibliography file and extract all citation keys.

  2. Scan lecture files for citation keys:

    • .tex: \cite{, \citet{, \citep{, \citeauthor{, \citeyear{, \textcite{, \parencite{
    • .qmd / .md: @key, [@key], [@key1; @key2]
    • Extract all unique citation keys used.
  3. Cross-reference:

    • Missing entries (CRITICAL): cited in lectures, absent from .bib.
    • Unused entries (informational): in .bib but never cited.
    • Typo candidates: keys within edit-distance 2 of a .bib key (e.g., Smith2020 vs Smth2020).
  4. Check entry quality:

    • Required fields present (author, title, year, journal/booktitle).
    • Author field properly formatted.
    • Year in 1900–current.
    • No malformed characters / encoding issues.
    • doi field normalized (no leading https://doi.org/).
  5. Write report to quality_reports/bib_audit_structural.md.

Files scanned
Slides/*.tex
Quarto/*.qmd
guide/*.qmd
master_supporting_docs/**/*.tex
Bibliography location

Bibliography_base.bib at repo root by default; override via CLAUDE.md.

Mode 2: Semantic (--semantic)

Everything in Mode 1, plus:

2a. Citation drift detection

Multiple .bib entries describing the same paper under different keys. Symptoms:

  • Smith2020 + Smith2020a with identical DOI or title.
  • CallawaySantAnna2021 + CS2021 both pointing to the same paper.
  • Collaborator-merged .bib files.

Detection heuristics (any → FLAG):

CheckSignal
Same DOI across keysHard-duplicate (CRITICAL)
Same title (case-insensitive, punct-stripped)Likely duplicate (CRITICAL)
Same author+year+journalProbable duplicate (MEDIUM)
Title Jaccard > 0.85 on tokens ≥ 4 charsSoft-duplicate (LOW)

For each flagged pair: list both keys, where each is cited, and recommend a canonical key (prefer most-cited, then alphabetically first).

2b. DOI verification (optional; network)

For each entry with a doi, fetch https://api.crossref.org/works/{doi} and compare:

  • First-author last name
  • Year
  • Title (Jaccard > 0.7 on normalized tokens)
  • Container-title / journal (exact or abbreviation)

Severity:

  • Author or title mismatch → CRITICAL (wrong paper)
  • Year mismatch → MEDIUM (preprint vs published, or typo)
  • Journal mismatch → LOW (legitimate preprint variants)

Rate limit: cap 50 lookups per run, 0.5s delay between calls. Cache in quality_reports/.doi_cache.json.

Opt-out: --skip-doi for offline or no-WebFetch environments.

Show full SKILL.md (245 more words)Show less
2c. Style consistency within each file

For each file, count citation commands (\citet vs \citep vs \cite; @key vs [@key]). FLAG files with mixed styles without an obvious pattern (e.g., 20× \citep and 3× \cite in the same deck). Low-severity.

2d. Cite-claim sanity (flag-only)

Gated behind --cite-claim. For the top-10 most-cited works per file, WebFetch the crossref abstract and surface it beside the in-text context. No auto-judgment — humans decide if the claim matches.

This is existence/structure, not appropriateness. Deciding whether the cited paper actually says what the in-text claim attributes to it is /verify-claims's job — it reads the source and grounds a supports / partial / contradicts verdict in quotes + pages (with the EXPLAINED escape for a defensible named alternative). --cite-claim only surfaces the abstract; for the verdict, run /verify-claims.

Report structure (quality_reports/bib_audit_semantic.md)
markdown
# Bibliography Semantic Audit

**Date:** YYYY-MM-DD
**Bibliography:** Bibliography_base.bib (N entries)
**Files scanned:** [list]

## Summary

| Check | Critical | Medium | Low |
|---|---|---|---|
| Structural | | | |
| Citation drift | | | |
| DOI verification | | | |
| Style consistency | 0 | 0 | |

## Critical Issues

### Duplicate entries
| Keys | Signal | Citations | Recommended canonical |
|---|---|---|---|

### DOI mismatches
| Key | Field | .bib value | crossref value |
|---|---|---|---|

## Medium / Low issues
…

## Next steps
1. Resolve duplicates — pick canonical key, update citations, remove orphans.
2. Fix DOI mismatches — verify paper in crossref or strip the wrong DOI.
3. Review style-consistency notes.

Exit behavior

  • Structural: exit 0; report enumerates issues.
  • Semantic: exit 0 if only LOW findings; exit 1 on any CRITICAL. Usable as a pre-submission gate.

Cross-references

  • .claude/skills/review-paper/SKILL.md — pair for full pre-submission.
  • .claude/skills/audit-reproducibility/SKILL.md — numeric-claims counterpart.
  • .claude/skills/verify-claims/SKILL.md — citation appropriateness counterpart (does the cited paper support the claim?). This skill checks that a citation exists and is well-formed; /verify-claims checks that it holds.

What this skill does NOT do

  • Judge whether a citation is used in the right context — whether the cited paper actually says what the claim attributes to it. That is /verify-claims's job (see 2d); this skill stays existence-and-structure only.
  • Auto-fix your .bib file — all edits are recommendations.
  • Check non-DOI identifiers (ISBN, arXiv, SSRN) — roadmap.

© pedrohcgs, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/validate-bib of pedrohcgs/claude-code-my-workflow.

Open the folder on GitHubat commit ae72617

Compare with similar skills

Validate Bib next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Validate Bib compared with similar skills
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NetworkxzLanqing/codex-claude-academic-skills4.6k16 repos~3.2kAutomated safety check: PassBSD-3-Clause
Citation Verification GuideGalaxy-Dawn/claude-scholar5.7k3 repos~1.9kAutomated safety check: PassMIT
Systematic Review ScreenerImbad0202/academic-research-skills51k—~8.4kAutomated safety check: PassCustom licence
Literature Reviewneflibata-feng/MyArxiv-Agent12621 repos~5.9kAutomated safety check: NotesMIT

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Questions about Validate Bib

What does Validate Bib do?

Validate bibliography entries against citations in all lecture files. Validate Bib is an agent skill from pedrohcgs/claude-code-my-workflow. Validate bibliography entries against citations in all lecture files.

When should I use Validate Bib?

Validate Bib fits situations like: tasks that involve Citation management; tasks that involve GitOps.

How do I install Validate Bib in Claude Code?

Run `npx skills add pedrohcgs/claude-code-my-workflow --skill validate-bib -a claude-code`. Or copy the skill folder (.claude/skills/validate-bib in pedrohcgs/claude-code-my-workflow) into .claude/skills/validate-bib in your project. Claude Code loads it when a task matches its description.

How do I install Validate Bib in Codex?

Run `npx skills add pedrohcgs/claude-code-my-workflow --skill validate-bib -a codex`. Or copy the skill folder (.claude/skills/validate-bib in pedrohcgs/claude-code-my-workflow) into .agents/skills/validate-bib in your project. Codex loads it when a task matches its description.

Can I use Validate Bib in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add pedrohcgs/claude-code-my-workflow --skill validate-bib -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/validate-bib, .gemini/skills/validate-bib, .github/skills/validate-bib and .opencode/skills/validate-bib in your project.

What does Validate Bib need to run?

SKILL.md names no scripts, command-line tools or credentials: Validate Bib is instructions for the agent only. Its frontmatter pre-approves these tools: Read, Grep, Glob, Write, Bash, WebFetch.

Does Validate Bib access the network?

SKILL.md names 2 domains. In commands or code: doi.org and api.crossref.org; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.

Is Validate Bib safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Validate Bib use?

Validate Bib is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Validate Bib use?

About 1.5k tokens (SKILL.md is roughly 6.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Validate Bib?

Skills that share tags, products or a category with Validate Bib: Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars), Networkx (zLanqing/codex-claude-academic-skills, 4.6k stars), Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars) and Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Validate Bib?

pedrohcgs (a GitHub user) maintains it in pedrohcgs/claude-code-my-workflow, which has 1,645 GitHub stars. The repository holds 59 skills in this directory. The repository was last updated on September 27, 2026.

Source: pedrohcgs/claude-code-my-workflow on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.