| 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:
-
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.
-
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.
-
Extract all bibliography entries — Parse the References section. Extract author surname(s), year, and title from each entry. Generate matching lookup keys.
-
Cross-reference: citations → bibliography — For each inline citation, find the matching bibliography entry. Record any citations that have no match ("cited but not listed").
-
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").
-
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.
-
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:
-
Run audit (if not already done) to identify all issues.
-
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)
-
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
-
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)
-
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:
-
Identify the target style — Use the --style flag (apa, vancouver, chicago) or detect from the manuscript. See REFERENCE_STYLES.md.
-
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
-
Check inline citations for style consistency:
- Correct use of
& vs. and
- Correct et al. threshold
- Correct punctuation within parenthetical citations
-
Report issues with specific entries and the required corrections.
-
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:
Related Files
