bibliography

name	bibliography
description	Audit, fix, and format bibliographies for academic manuscripts. Cross-references inline citations against the reference list to find orphans in both directions. Complements scientific-style (citation prose quality) and submission-prep (formatting checklists).
argument-hint	["audit manuscript.md or format --style apa manuscript.md"]

Bibliography Skill

Audit, fix, and format bibliographies for academic manuscripts.

When to Use This Skill

• Checking that every inline citation has a matching bibliography entry
• Finding bibliography entries that are never cited in the text
• Catching informal author mentions that lack formal citations
• Standardizing reference formatting to a target style (APA, Vancouver, Chicago)
• Preparing a manuscript for submission (pair with submission-prep)

Combine with: scientific-style for citation prose quality (reporting verbs, integral vs. non-integral), submission-prep for journal-specific formatting requirements.

Three Modes

1. Audit Mode (default)

Perform a bidirectional cross-reference check. This is the core function.

Invoke with: /bibliography audit manuscript.md

Procedure:

1. Identify the citation system — Read the first 3-5 inline citations. Classify as author-year (APA/Harvard), numbered (Vancouver), or other. See CITATION_FORMATS.md.

2. Extract all inline citations — Scan the entire body text (everything above the References/Bibliography section). For author-year systems, capture both parenthetical (Smith, 2024) and narrative Smith (2024) forms. For numbered systems, capture all [N] references. Normalize each to a lookup key.

3. Extract all bibliography entries — Parse the References section. Extract author surname(s), year, and title from each entry. Generate matching lookup keys.

4. Cross-reference: citations → bibliography — For each inline citation, find the matching bibliography entry. Record any citations that have no match ("cited but not listed").

5. Cross-reference: bibliography → citations — For each bibliography entry, find at least one matching inline citation. Record any entries with no match ("listed but not cited").

6. Scan for informal mentions — Build a surname list from the bibliography. Scan body text for these surnames appearing outside of formal citations. Flag instances like "Tufte argued that..." where a formal citation is missing.

7. Generate the audit report — Use the template in AUDIT_REPORT_TEMPLATE.md. Include counts, status assessment, and specific issues with locations.

The bidirectional check:

  BODY TEXT                          BIBLIOGRAPHY
  ─────────                          ────────────
  (Smith, 2024)  ──────────────────► Smith, J. (2024)...     ✓
  (Jones, 2023)  ──────────────────► Jones, K. (2023)...     ✓
  Lee (2024)     ───── ? ──────────►                         ✗ CITED BUT NOT LISTED
                                     Adams, R. (2022)...     ✗ LISTED BUT NOT CITED
  "Tufte argued" ─── informal ─────►                         ⚠ INFORMAL MENTION

2. Fix Mode

Resolve issues found during audit. Always run audit first.

Invoke with: /bibliography fix manuscript.md

Procedure:

1. Run audit (if not already done) to identify all issues.

2. Cited but not listed — For each missing entry:

   • Search for the full reference details in the manuscript context (footnotes, supplementary material, or related files)
   • If details are available, add a properly formatted entry to the bibliography
   • If details are unknown, add a placeholder: [TODO: Complete reference for Smith (2024)]
   • Place the entry in correct order (alphabetical for author-year, sequential for numbered)

3. Listed but not cited — For each orphaned entry:

   • Read the entry's title and topic
   • Scan the manuscript for passages where this reference is relevant
   • If a relevant passage exists, add an inline citation at the appropriate location
   • If no relevant passage exists, flag the entry for potential removal but do NOT remove automatically — the author may intend to cite it in a future revision

4. Informal mentions — For each informal mention:

   • Identify the referenced work (match to bibliography or determine the needed reference)
   • Convert to a formal citation: "Tufte argued..." → "Tufte (2001) argued..."
   • If the work is not in the bibliography, add it (see step 2)

5. Re-run audit to verify all issues are resolved. Report the before/after comparison.

3. Format Mode

Validate and standardize reference formatting to a target style.

Invoke with: /bibliography format --style apa manuscript.md

Procedure:

1. Identify the target style — Use the --style flag (apa, vancouver, chicago) or detect from the manuscript. See REFERENCE_STYLES.md.

2. Check each bibliography entry against the target style rules:

   • Author name format (initials vs. full names, punctuation)
   • Year placement
   • Title capitalization (sentence case vs. title case)
   • Journal name formatting (italics, abbreviation)
   • Volume/issue/page format
   • DOI format
   • Punctuation and ordering

3. Check inline citations for style consistency:

   • Correct use of & vs. and
   • Correct et al. threshold
   • Correct punctuation within parenthetical citations

4. Report issues with specific entries and the required corrections.

5. Apply corrections if requested, preserving the semantic content while fixing formatting.

Boundary with Other Skills

Concern	Skill
Whether a citation exists and is linked to a bibliography entry	bibliography
Reference formatting correctness (APA, Vancouver, etc.)	bibliography
How to integrate a citation into prose (integral vs. non-integral)	scientific-style
Reporting verb choice ("found" vs. "demonstrated")	scientific-style
Overall submission checklist (figures, cover letter, etc.)	submission-prep
Claim calibration (hedging strength)	scientific-style

Common Problems

Problem	Detection	Fix
Cited but not listed	Citation in text, no matching bibliography entry	Add bibliography entry
Listed but not cited	Bibliography entry, no inline citation	Add citation or flag for removal
Informal mention	Author surname in text without (YYYY)	Convert to formal citation
Duplicate entries	Same work listed twice with slight variations	Merge into single entry
Inconsistent style	Mix of APA and Vancouver formatting	Standardize to one style
Wrong et al. usage	Too few authors for et al. (APA: need 3+)	List all authors or use correct threshold
Broken numbering	Vancouver numbers skip or repeat	Renumber sequentially
Year mismatch	Inline says 2024, bibliography says 2023	Verify correct year and fix
Author name mismatch	Inline says "Smith" but entry is "Smyth"	Verify correct spelling

Handling Edge Cases

Multiple Works by Same Author in Same Year

• APA: (Smith, 2024a) and (Smith, 2024b) — add letter suffixes
• Vancouver: separate numbers, no special handling needed
• Chicago: (Smith 2024a) and (Smith 2024b)

Secondary Citations (Citing Through Another Work)

• APA: (Smith, 2020, as cited in Jones, 2024) — only Jones appears in bibliography
• Flag if Smith also appears in bibliography (redundant)

Works with No Author

• APA: Use title in citation: ("Article Title," 2024)
• Vancouver: Organization name or title
• Match carefully — these are easy to miss in cross-referencing

Manuscripts with .bib Files

• Check the .bib file for all entries
• Also check the rendered bibliography (some .bib entries may not be \cited)
• Keys like \cite{smith2024} map to @article{smith2024,...} in the .bib file

Quality Checks

Before finalizing any bibliography work:

• Every inline citation matches exactly one bibliography entry
• Every bibliography entry is cited at least once
• No informal author mentions without formal citations
• Entries follow a single, consistent style
• Entry ordering matches the style (alphabetical or by appearance)
• Author names are spelled consistently between inline citations and bibliography
• Years match between inline citations and bibliography entries
• For numbered systems: numbers are sequential with no gaps or duplicates
• For author-year systems: entries with same author/year have letter suffixes (a, b, c)
• DOIs are included where available

Related Files

• CITATION_FORMATS.md — Detection patterns for citation and bibliography formats
• REFERENCE_STYLES.md — APA, Vancouver, Chicago formatting rules
• AUDIT_REPORT_TEMPLATE.md — Structured output template for audit results