How to install citation-management
npx skills add https://github.com/lingzhi227/agent-research-skills --skill citation-managementFull instructions (SKILL.md)
Source of truth, from lingzhi227/agent-research-skills.
name: citation-management description: Manage BibTeX citations for LaTeX papers. Harvest missing citations from a draft using Semantic Scholar, validate cite keys against .bib files, deduplicate entries, and format bibliography. Use when working with references, BibTeX, or citations. argument-hint: [tex-or-bib-file]
Citation Management
Manage the full lifecycle of citations in a LaTeX paper.
Input
$0— Action:harvest,validate,add,format$1— Path to.texor.bibfile
Scripts
Validate citations (check all cite keys resolve)
python ~/.claude/skills/citation-management/scripts/validate_citations.py \
--tex paper/main.tex --bib paper/references.bib --check-figures --figures-dir paper/figures/
Reports: missing citations, unused bib entries, duplicate keys, duplicate sections, duplicate labels, undefined references, missing figures.
Generate BibTeX from paper database
python ~/.claude/skills/deep-research/scripts/bibtex_manager.py \
--jsonl paper_db.jsonl --output references.bib
Search for a specific paper to add
python ~/.claude/skills/deep-research/scripts/search_semantic_scholar.py \
--query "attention is all you need" --max-results 5 \
--api-key "$(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:
- Read the current
.texdraft - Identify the most important missing citation
- Search Semantic Scholar via script
- Select the most relevant paper from results
- Extract BibTeX and generate a clean key (
lastNameYearWord) - Append to
.bib(skip if key exists) - Insert
\cite{key}at the appropriate location - 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
Related skills
More from lingzhi227/agent-research-skills and the wider catalog.
code-debugging
Debug experiment code with structured error analysis. Categorize errors, apply targeted fixes with retry logic, and use reflection to prevent recurring issues. Use when experiment code fails or produces incorrect results.
data-analysis
Generate statistical analysis code with 4-round review. Select appropriate statistical tests, interpret results, and produce analysis reports with p-values, effect sizes, and confidence intervals. Use when analyzing experimental data for a paper.
deep-research
Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Output is organized by phase for clarity.
excalidraw-skill
Programmatic canvas toolkit for creating, editing, and refining Excalidraw diagrams via MCP tools with real-time canvas sync. Use when an agent needs to (1) draw or lay out diagrams on a live canvas, (2) iteratively refine diagrams using describe_scene and get_canvas_screenshot to see its own work, (3) export/import .excalidraw files or PNG/SVG images, (4) save/restore canvas snapshots, (5) convert Mermaid to Excalidraw, or (6) perform element-level CRUD, alignment, distribution, grouping, duplication, and locking. Requires a running canvas server (EXPRESS_SERVER_URL, default http://localhost:3000).
experiment-code
Write ML experiment code with iterative improvement. Generate training/evaluation pipelines, debug errors, and optimize results through code reflection. Use when implementing experiments for a research paper.
experiment-design
Design experiment plans with progressive stages — initial implementation, baseline tuning, creative research, and ablation studies. Plan baselines, datasets, hyperparameter sweeps, and evaluation metrics. Use when planning experiments for a research paper.