Citation Engine

If a match is found, retrieve full metadata with mcp__plugin_pubmed_PubMed__get_article_metadata or mcp__claude_ai_PubMed__get_article_metadata. Extract: authors, title, journal, year, volume, issue, pages, DOI, PMID.

Fallback trigger: No results returned, OR metadata missing title/authors/year. Proceed to Step 2.

Step 2 — CrossRef (second)

Use WebFetch to query the CrossRef API:

URL: https://api.crossref.org/works?query=<URL-encoded-title>&rows=3

Parse the JSON response. For each item in message.items[], extract:

• DOI — the DOI string
• author[] — each entry has given and family fields
• title[] — article title (first element)
• container-title[] — journal name (first element)
• published.date-parts[] — year from first element
• volume — volume number
• issue — issue number
• page — page range

Match by comparing title similarity (case-insensitive, ignoring punctuation). Accept if title similarity >85%.

Fallback trigger: No results returned, OR title similarity <85% for all results, OR metadata missing title/authors/year. Proceed to Step 3.

Step 3 — Semantic Scholar (third)

Use WebFetch to query the Semantic Scholar API:

URL: https://api.semanticscholar.org/graph/v1/paper/search?query=<URL-encoded-title>&limit=3&fields=title,authors,year,venue,externalIds

Parse the JSON response. For each item in data[], extract:

• paperId — Semantic Scholar paper ID
• title — article title
• authors[].name — author names
• year — publication year
• venue — journal or conference name
• externalIds.DOI — DOI (if available)
• externalIds.PubMed — PMID (if available)

Fallback trigger: No results returned, OR metadata missing title/authors/year. Proceed to Step 4.

Step 4 — bioRxiv/medRxiv (fourth)

Use mcp__claude_ai_bioRxiv__search_preprints to search for the article. If found, retrieve full metadata with mcp__claude_ai_bioRxiv__get_preprint.

Additionally, use mcp__claude_ai_bioRxiv__search_published_preprints to check whether the preprint has been formally published in a peer-reviewed journal.

Fallback trigger: No results returned across any source. Mark citation as unverified (see Section 6).

2. Metadata Normalisation

After retrieval from any source, normalise all citation metadata into the following standardised fields:

Author Name Normalisation

• Extract last name and initials from each source format:
  • PubMed: typically provides "LastName Initials" directly
  • CrossRef: combine family + first letter(s) of given
  • Semantic Scholar: parse "FirstName LastName" → "LastName F"
  • bioRxiv: parse as available
• Remove periods from initials (e.g., "Page MJ" not "Page M.J.")
• Preserve hyphenated surnames: "García-López A"
• Preserve multi-part surnames: "van der Berg A", "de Souza M"

3. Duplicate Detection

When the same paper is found across multiple databases, merge records to produce the most complete metadata set.

Detection criteria (any one is sufficient):

• DOI exact match (case-insensitive)
• Title similarity >90% (case-insensitive, ignoring punctuation and whitespace differences)

Merge strategy:

1. Prefer PubMed metadata when available (most authoritative for biomedical literature)
2. Fill missing fields from CrossRef (best for DOI and page ranges)
3. Fill remaining gaps from Semantic Scholar
4. Use bioRxiv only for preprint-specific information

4. Preprint Status Check

When a citation is found on bioRxiv or medRxiv:

1. Run mcp__claude_ai_bioRxiv__search_published_preprints with the preprint DOI or title
2. If a published version exists:
   • Retrieve the published version's metadata via PubMed or CrossRef
   • Suggest to the user: [NOTE: This preprint has been published as: <full published reference>. Consider updating the citation.]
3. If no published version exists:
   • Include the preprint citation with the bioRxiv/medRxiv DOI
   • Add a note: [Preprint — not yet peer-reviewed]

5. Cross-Referencing

After all references are formatted, perform a bidirectional audit:

In-text to reference list

• For every in-text citation number (e.g., [1], [2], [1-3]), confirm a corresponding entry exists in the reference list
• Flag missing: [WARNING: In-text citation [N] has no matching reference]

Reference list to in-text

• For every reference in the list, confirm it is cited at least once in the text
• Flag orphans: [WARNING: Reference N is listed but never cited in-text]

Numbering integrity

• Verify citation numbers are sequential (1, 2, 3, ...) with no gaps
• Verify numbers follow order of first appearance in the text
• Flag any discontinuities

6. Unverifiable Citations

When a citation cannot be verified through any of the four pipeline sources:

[UNVERIFIED — not found in PubMed, CrossRef, Semantic Scholar, or bioRxiv. Please check manually]

This flag is appended after the reference entry. The reference is retained exactly as the user provided it, but the flag alerts to manual verification need.

Never fabricate. If the user provides incomplete citation information and no database match is found, do not guess missing fields. Instead:

• Retain what the user provided
• Mark missing fields: [year unknown], [volume/pages unknown], [DOI unknown]
• Append the [UNVERIFIED] flag

7. Citation Style Formatting

The citation style is determined by:

1. citation_style field in PAPER_CONTEXT.md (if present)
2. User request (e.g., "format in APA style")
3. Default: Vancouver

See references/citation-styles.md for complete formatting rules and examples for all six supported styles:

8. Workflow Integration

When invoked by /write-references or "write references"

1. Collect all in-text citations from the manuscript
2. Run each through the verification pipeline (Section 1)
3. Normalise metadata (Section 2)
4. Detect and merge duplicates (Section 3)
5. Check preprint status (Section 4)
6. Format in the selected citation style (Section 7)
7. Cross-reference in-text numbers against the list (Section 5)
8. Output the formatted reference list with any flags

When invoked by /verify-citations or "verify citations"

1. Parse the existing reference list
2. Run each reference through the verification pipeline
3. Report verification status for each reference:
   • Verified: metadata confirmed against database
   • Partial: some fields confirmed, others unverifiable
   • Unverified: no database match found
4. Suggest corrections for any discrepancies found

9. Error Handling

References

• references/citation-styles.md — Full formatting rules for all 6 citation styles