BibTeX Curator

Detect written-out citations in .qmd/.tex files, resolve them to BibTeX entries, replace with proper citation commands, and check working papers for published versions.

Prerequisites

Requires 3 MCP servers (see ../../mcps/README.md for installation):

•semantic-scholar-mcp — search academic papers, retrieve BibTeX
•crossref-mcp — search metadata, get BibTeX, find published versions
•bibtex-mcp — parse .bib files, scan documents, rekey entries, generate cite commands

Constraints

•NEVER change the meaning of a citation (wrong paper is worse than a bare citation)
•NEVER delete existing proper citations (@key, \cite{key}, etc.)
•MUST preserve all surrounding text exactly
•MUST add new entries to the project's existing .bib file (don't create a new one)
•MUST match the project's existing BibTeX key convention (observe existing keys before generating new ones)

Escalation Policy

Ask the user when:

•Multiple .bib entries match the same author-year
•API confidence score is 4–6 (ambiguous match)
•Author name could refer to different people (e.g., "Smith (2015)")
•Can't find the paper through any source
•A working paper's published version has a substantially different title (similarity < 0.8)

Proceed automatically when:

•Unique match found in .bib file
•High-confidence API match (score >= 7)
•Straightforward citation syntax replacement
•Working paper clearly published with same/near-identical title (similarity >= 0.8)

Workflow

Step 1: Locate Document and Bibliography

Goal: Identify what document to fix and where its bibliography file is

Detect document type:

•.qmd file → Quarto (uses @key syntax)
•.tex file → LaTeX (uses \citet{key} or \citep{key} syntax)

Locate bibliography file:

•For .qmd: Extract from bibliography: field in YAML frontmatter
•For .tex: Extract from \bibliography{filename} command
•If not found, ask user for the path to their .bib file

Step 2: Scan for Bare Citations

Goal: Find all written-out citations (like "Author (Year)") that need to be converted to proper citation commands

Use bibtex-mcp tool:

code

bibtex-mcp.scan_bare_citations(path: document_path)

Returns array of citations with:

•text — matched citation text (e.g., "Conley and Udry (2010)")
•line — line number in document
•authors — extracted author last names
•year — extracted year
•citation_type — "narrative" or "parenthetical"
•locator — page/chapter reference if present
•prefix, suffix — additional text like "see" or "among others"

This gives us a to-do list of all citations that need fixing. Report to user: "Found N bare citations to resolve."

Step 3: Parse Existing Bibliography

Goal: Index the existing .bib file so we can check if papers are already there before searching APIs

Use bibtex-mcp tool:

code

bibtex-mcp.parse_bib(path: bib_file_path)

Returns author-year index mapping strings like "Conley-2010" to arrays of matching entries. Each entry includes:

•key — BibTeX key (e.g., "conley2010learning")
•type — entry type (article, techreport, unpublished, etc.)
•authors — array of author last names
•year, title, fields

This lets us quickly check "is Conley (2010) already in the .bib?" before doing expensive API searches.

Step 4: Resolve Each Citation

Goal: For each bare citation, figure out which paper it refers to and get its proper BibTeX key

For each bare citation detected in Step 2, resolve in priority order:

Priority 1: Existing .bib Match

Check if the citation's authors and year match any entry in the parsed bibliography index (from Step 3).

If unique match found:

•Use bibtex-mcp tool to generate replacement:

code

bibtex-mcp.suggest_replacement(
  citation_text: original_text,
  key: matched_bib_key,
  doc_type: "qmd" or "tex",
  natbib: true
)

•Replace the bare citation with the suggested command
•Continue to next citation

If multiple matches found:

•Show user the options with titles
•Ask which entry they meant
•Use selected key for replacement

If no match found:

•Proceed to Priority 2 (Project markdown search)

Priority 2: Project Markdown Search

Goal: Check if you've written about this paper in project notes/summaries before searching external APIs

Grep the project directory for markdown files mentioning the author + year:

bash

grep -ri "Conley.*2010\|2010.*Conley" *.md --exclude=paper.qmd

Look for context like:

•Paper titles in headers or bullet points
•Journal names, DOIs, or working paper series
•Your own summaries or notes about the paper

If context found:

•Extract title/journal/DOI from the markdown context
•Ask user: "Found in your notes: '[title]'. Is this the paper you're citing?"
•If confirmed, search CrossRef/Semantic Scholar with the extracted title for validation
•Get BibTeX and proceed to Step 5 (Add Entry)

If no useful context found:

•Proceed to Priority 3 (API search)

Priority 3: API Search

Goal: Search external APIs when the paper isn't in your .bib or notes

Try CrossRef first (better for economics papers):

code

crossref-mcp.search(
  query: "{first_author} {title_keywords}",
  author: "{first_author}",
  year: {year},
  rows: 5
)

Each result includes a confidence_score (0-9) computed by the server:

•Author match: +3
•Year match: +2
•Title keywords: +2
•Has DOI: +1
•Is journal-article: +1

If confidence >= 7:

•Get BibTeX: crossref-mcp.get_bibtex(doi: result.doi)
•Proceed to Step 5 (Add Entry)

If confidence 4-6:

•Show user top 3 results with titles and confidence scores
•Ask which is correct (or none)
•Get BibTeX for selected result

If confidence < 4 or no results:

•Try Semantic Scholar:

code

semantic-scholar-mcp.search(
  query: "{authors} {year} {title_keywords}",
  year: "{year}",
  limit: 5
)

•Follow same confidence logic
•Get BibTeX: semantic-scholar-mcp.get_bibtex(paper_id: result.paperId)

If still no match:

•Ask user if they can provide more context (title, journal, DOI)
•Try API search again with additional info
•Or ask user to manually add the entry

Step 5: Add New Entries to Bibliography

Goal: Add newly-found papers to the .bib file with properly formatted keys that match the project's convention

For entries found via API (in Step 4):

•
Get raw BibTeX (already done in Step 4)

•

Rekey to match project convention:

code

bibtex-mcp.rekey_entry(
  bibtex: raw_bibtex_string,
  existing_keys: [list_of_all_keys_from_step_3],
  convention: "auto"
)

Returns BibTeX with key rewritten to match project's format (e.g., conley2010learning)

•

Add to .bib file:

code

bibtex-mcp.add_entry(
  bib_path: bib_file_path,
  entry: rekeyed_bibtex
)

•

Generate citation command:

code

bibtex-mcp.suggest_replacement(
  citation_text: original_text,
  key: new_key,
  doc_type: "qmd" or "tex",
  natbib: true
)

•
Replace bare citation in the document with the suggested command

Step 6: Check Working Papers for Published Versions

Goal: Find if any unpublished papers in the .bib have since been published, so we can upgrade them to the published version

After resolving all citations, scan the .bib file for unpublished papers:

For each @techreport or @unpublished entry:

code

crossref-mcp.find_published_version(
  title: entry.title,
  author: entry.first_author,
  working_paper_year: entry.year
)

Returns published version with:

•Metadata (title, authors, journal, year, DOI)
•bibtex — BibTeX entry for published version
•Title similarity score

If found and similarity >= 0.8:

•Show user the working paper and published version
•Ask if they want to upgrade
•If yes, use bibtex-mcp.rekey_entry() and replace in .bib

If found and similarity < 0.8:

•Show both, note the title difference
•Ask user to verify it's the same paper
•Proceed if confirmed

If not found:

•No action (working paper remains as-is)

Step 7: Final Report

Goal: Summarize what was accomplished

Report to user:

code

📊 Citation Curation Complete

Bare citations: X found, Y resolved
- Z resolved from existing .bib
- W resolved from CrossRef
- V resolved from Semantic Scholar
- U required user input

Working papers checked: N
- M upgraded to published versions
- P remain unpublished

Changes:
- Added Q new entries to bibliography.bib
- Replaced X bare citations with proper commands

Example Session

code

User: "Fix the citations in paper.qmd"

Step 1: Found bibliography: references.bib

Step 2: Scan document
Found 5 bare citations:
   - Line 12: "Conley and Udry (2010)"
   - Line 45: "(Banerjee et al. 2013)"
   - ...

Step 3: Parsed references.bib → 47 entries indexed

Step 4: Resolve citations

   ✓ "Conley and Udry (2010)" → matched existing key `conley2010learning`
     Replaced with: @conley2010learning

   ✓ "Banerjee et al. (2013)" → not in .bib, searching APIs...
     CrossRef match (score 8): "The Miracle of Microfinance?"
     Added as `banerjee2013miracle`
     Replaced with: [@banerjee2013miracle]

   [... 3 more citations ...]

Step 6: Check working papers: 3 found
   ✓ "Mogstad (2012)" NBER → found published in AER 2015
     Upgraded to journal article

📊 Complete: 5/5 citations resolved, 1 working paper upgraded

Notes on Citation Commands

Quarto Syntax

•Narrative: @key → renders as "Author (Year)"
•Parenthetical: [@key] → renders as "(Author Year)"
•With locator: [@key, p. 45]
•Multiple: [@key1; @key2]
•Year-only: [-@key]

LaTeX/natbib Syntax

•Narrative: \citet{key} → renders as "Author (Year)"
•Parenthetical: \citep{key} → renders as "(Author Year)"
•With locator: \citep[p. 45]{key}
•Multiple: \citep{key1, key2}
•Possessive: \citeauthor{key}'s (\citeyear{key})

The bibtex-mcp.suggest_replacement() tool handles these conversions automatically.

Troubleshooting

Issue: scan_bare_citations returns false positives

•Check if citation is in acknowledgments or author list (tool should exclude these)
•Verify citation isn't already proper (@key or \cite{})
•Some matches may be non-citation mentions (e.g., "World Bank (2020 fiscal year)") — skip these

Issue: Can't find paper via any API

•Ask user for DOI or full title
•Search with more specific query
•User may need to manually create entry

Issue: Multiple .bib entries with same author-year

•Show user all matching entries with titles
•Let user choose the correct one
•Never guess — wrong citation is worse than bare citation

Reference Files (Legacy)

The references-legacy/ directory contains the original implementation documentation:

•citation-patterns.md — regex patterns (now in bibtex-mcp.scan_bare_citations())
•api-lookups.md — API instructions (now in crossref-mcp and semantic-scholar-mcp tools)
•bibtex-formats.md — key generation rules (now in bibtex-mcp.rekey_entry())

These files are preserved for historical reference. The logic has been moved into the MCP servers for deterministic, testable implementation.