lingzhi227/agent-research-skills/citation-management

Citation Management

Manage the full lifecycle of citations in a LaTeX paper.

Input

• $0 — Action: harvest, validate, add, format
• $1 — Path to .tex or .bib file

Scripts

Validate citations (check all cite keys resolve)

python ~/.claude/skills/citation-management/scripts/validate_citations.py \
  --tex paper/main.tex --bib paper/references.bib --check-figures --figures-dir paper/figures/

Reports: missing citations, unused bib entries, duplicate keys, duplicate sections, duplicate labels, undefined references, missing figures.

Generate BibTeX from paper database

python ~/.claude/skills/deep-research/scripts/bibtex_manager.py \
  --jsonl paper_db.jsonl --output references.bib

Search for a specific paper to add

python ~/.claude/skills/deep-research/scripts/search_semantic_scholar.py \
  --query "attention is all you need" --max-results 5 \
  --api-key "$(grep S2_API_Key /Users/lingzhi/Code/keys.md 2>/dev/null | cut -d: -f2 | tr -d ' ')"

Harvest missing citations automatically

python ~/.claude/skills/citation-management/scripts/harvest_citations.py \
  --tex paper/main.tex --bib paper/references.bib --output candidates.bib --max-rounds 10

Scans .tex for uncited claims, searches Semantic Scholar, outputs candidate BibTeX entries. Key flags: --dry-run (preview only), --verbose, --api-key

Auto-fix missing citation placeholders

python ~/.claude/skills/citation-management/scripts/validate_citations.py \
  --tex paper/main.tex --bib paper/references.bib --fix

Generates references_fixed.bib with placeholder entries for all missing citation keys.

Action: harvest — Iterative Citation Harvesting

Based on AI-Scientist's 20-round citation harvesting loop. For each round:

1. Read the current .tex draft
2. Identify the most important missing citation
3. Search Semantic Scholar via script
4. Select the most relevant paper from results
5. Extract BibTeX and generate a clean key (lastNameYearWord)
6. Append to .bib (skip if key exists)
7. Insert \cite{key} at the appropriate location
8. Stop when no more gaps or 20 rounds reached

Key rules:

• DO NOT add a citation that already exists
• Only add citations found via API — never fabricate
• Cite broadly — not just popular papers
• Do not copy verbatim from prior literature

Action: validate — Pre-Compilation Check

Run validate_citations.py to catch all issues before compilation. Fix any reported problems.

Action: add — Add Specific Paper

Search Semantic Scholar for the paper, extract BibTeX, clean the key, append to .bib.

BibTeX key format: firstAuthorLastNameYearFirstContentWord (e.g., vaswani2017attention)

Action: format — Standardize .bib

• Sort entries alphabetically by key
• Ensure consistent indentation (2 spaces)
• Remove empty fields
• Protect proper nouns with {Braces} in titles
• Ensure required fields per entry type

Related Skills

• Upstream: literature-search, deep-research
• Downstream: paper-compilation, latex-formatting
• See also: related-work-writing