Dr Cook:citation Checker

citation-checker

1. Overview

Validates reference lists and in-text citations against Vancouver, APA 7th, and GB/T 7714-2015. Identifies formatting errors, orphaned citations, and self-citation rate violations. Operates standalone (user pastes text) or in pipeline mode (receives raw_text and references from upstream). Output: numbered issues list with severity tags and a corrected reference list. Bilingual input supported. Domains: tcm, bioinformatics, clinical, pharmacology.

2. Parameters

Required

Optional

Parameter collection rule

Collect one missing required parameter at a time. If citation_style and text are both available from upstream context_output, proceed without prompting. If check_self_citation = true but author_name is missing, ask for it before Step 6.

3. Workflow

Step 1 — Check for upstream context_output.

Inspect active context_output. Inherit parameters.citation_style → citation_style, parameters.domain → domain, raw_text → text, references → structured reference list. Record inherited fields for the output header. If no upstream context, proceed to Step 2.

Step 2 — Collect missing parameters.

• If citation_style not inherited, ask: "Which citation style: Vancouver, APA 7th, or GB/T 7714-2015?"
• Resolve text using the first available source: (1) context_output.raw_text if present; (2) text pasted directly in the user's message; (3) content the user references as "the file I shared" or a previously-displayed block — acknowledge and use it. If none apply, ask: "Please paste the reference list and/or manuscript text you'd like me to check."
• Collect one parameter at a time.
• If check_self_citation = true, ask for author_name immediately after confirming.
• If the user has not mentioned self-citation checking, briefly offer it after confirming citation_style and text are in hand: "Would you also like me to check the self-citation rate? If so, please provide your name as it appears in your publications."

Step 3 — Load citation format rules.

Load references/citation-formats.md. Extract the rule set for the selected citation_style (field-order, author format, DOI format, in-text regex patterns). Keep active through Steps 4 and 5.

Step 4 — Run format consistency check.

Parse the reference list from text (or references array if inherited). For each entry apply the rule set from Step 3: field order, author format and "et al" threshold, journal name (abbreviated vs. full), DOI format, punctuation, and GB/T 7714 document type identifier.

Severity: ERROR (missing required field, wrong field order, wrong type identifier); WARNING (wrong punctuation, DOI format mismatch, journal name not abbreviated when required); INFO (stylistic inconsistency not violating the standard).

Step 5 — Run in-text citation matching.

Extract all in-text markers using patterns from references/citation-formats.md. Style-specific rules apply:

• Vancouver and GB/T 7714: extract numeric markers using the bracket-number regex patterns from citation-formats.md.
• APA: build a surname-year lookup key for each reference (e.g., "Smith 2022"). Scan manuscript text for (Author, Year) patterns. When "et al." appears, match on first-author surname only (applies when ≥3 authors). Flag references with no match in text (orphan). Flag in-text citations with no reference list entry (dangling).

Compare in both directions:

• Cited in-text but absent from list → ERROR: "In-text citation [X] has no corresponding reference list entry."
• In list but never cited in-text → WARNING: "Reference [X] is never cited in the text."

Step 6 — Self-citation audit (conditional).

Run only if check_self_citation = true. Load references/self-citation-norms.md. Match author_name (surname + initials, fuzzy, case-insensitive) against each reference's author fields. Calculate rate: self_citations / total_references × 100%. Apply thresholds from norms file (defaults: > 30% ALERT; > 20% WARNING; ≤ 20% INFO). List matched references by number.

Step 7 — Output.

Present output per Section 4. Write context_output per Section 5.

4. Output Format

Output consists of two mandatory sections, presented in this order.

Section A — Issues Found

## Issues Found

[N issue(s) detected]

1. [SEVERITY] Reference N: description of issue.

If no issues are found: state "No citation issues found." then proceed to Section B.

Section B — Corrected Reference List

Echo the full reference list with all corrections applied inline. Number each entry. If a correction was applied, append [corrected] in italics after the entry on the same line for traceability.

If check_self_citation was run, append a Self-Citation Summary block after Section B showing: total references, self-citation count, rate percentage, severity level, and list of self-cited reference numbers.

5. context_output

Reads from upstream

Writes to output

{
  "module": "citation-checker",
  "summary": "string — one sentence: references checked, error/warning counts, self-citation rate if applicable.",
  "key_findings": [
    "string — one entry per ERROR-severity issue found"
  ],
  "references": [
    {
      "pmid": "string | null",
      "doi": "string | null",
      "title": "string",
      "authors": "string",
      "year": "integer"
    }
  ],
  "parameters": {
    "citation_style": "vancouver | apa | gb-t-7714",
    "domain": "tcm | bioinformatics | clinical | pharmacology | null",
    "self_citation_rate": "float | null — percentage value, e.g. 25.0; null if check_self_citation was false"
  },
  "status": "success | partial | failed",
  "error_message": "string | null — null on success; error description on failure"
}

• key_findings: ERROR-severity issues only; WARNING and INFO are in output text only.
• references: corrected reference list; replaces any upstream references array.
• status: "success" — completed; "partial" — some references unparseable; "failed" — no valid reference list found.

Downstream readers

references (corrected) → cover-letter-writer, grant-writer. summary and key_findings → paper-reviewer (if looping back for re-check).

6. References

• citation-formats.md — field-order rules, author format, DOI format, in-text regex patterns, and error checklists per style.
• self-citation-norms.md — rate thresholds by article type and journal tier, identification algorithm, and mitigation strategies.