Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation
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Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation
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Stars31,549
Forks3,146
LanguagePython
LicenseMIT
📦 Ships with scientific-agent-skills
</> SKILL.md
citation-management.SKILL.md
---name: citation-management
description: Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
allowed-tools: Read Write Edit Bash
license: MIT License
required_environment_variables: [{"name": "OPENROUTER_API_KEY", "prompt": "OpenRouter API key for LLM-powered citation steps.", "required_for": "optional features"}, {"name": "NCBI_EMAIL", "prompt": "Email for NCBI Entrez identification.", "required_for": "optional features"}, {"name": "NCBI_API_KEY", "prompt": "NCBI API key to raise Entrez rate limits.", "required_for": "optional features"}]
metadata: {"version": "1.3", "skill-author": "K-Dense Inc.", "openclaw": {"primaryEnv": "OPENROUTER_API_KEY", "envVars": [{"name": "OPENROUTER_API_KEY", "required": false, "description": "OpenRouter API key for LLM-powered citation steps."}, {"name": "NCBI_EMAIL", "required": false, "description": "Email for NCBI Entrez identification."}, {"name": "NCBI_API_KEY", "required": false, "description": "NCBI API key to raise Entrez rate limits."}]}}
---# Citation Management
## Overview
Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic databases (Google Scholar, PubMed), extracting accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validating citation information, and generating properly formatted BibTeX entries.
Critical for maintaining citation accuracy, avoiding reference errors, and ensuring reproducible research. Integrates seamlessly with the literature-review skill for comprehensive research workflows.
## When to Use This Skill
Use this skill when:
- Searching for specific papers on Google Scholar or PubMed
- Converting DOIs, PMIDs, or arXiv IDs to properly formatted BibTeX
- Verifying that citation information matches the actual publication
- Building a bibliography for a manuscript or thesis
- Checking for duplicate citations
- Ensuring consistent citation formatting
## Visual Enhancement with Scientific Schematics
**When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.**
If your document does not already contain schematics or diagrams:
- Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
- Simply describe your desired diagram in natural language
- Nano Banana Pro will automatically generate, review, and refine the schematic
**For new documents:** Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.
- **Preprints**: repository (arXiv, bioRxiv), preprint ID
- **Additional**: abstract, keywords, URL
### Phase 2.5: Metadata Enrichment via Web Search (MANDATORY)
**Goal**: Detect and fill in any missing metadata fields using web search. This phase runs AFTER extraction and BEFORE formatting to ensure every BibTeX entry is complete.
**Why This Is Critical**: Metadata extraction from APIs (CrossRef, PubMed, arXiv) sometimes returns incomplete records — missing volume, pages, issue number, or DOI. These gaps must be filled before the bibliography is considered ready.
#### Step 1: Scan for Incomplete Entries
After extracting metadata, scan the BibTeX file for entries missing key fields:
**Fields to check per entry type:**
| Entry Type | Must Have | Should Have |
|------------|-----------|-------------|
| @article | author, title, journal, year | volume, pages, number, doi |
| @inproceedings | author, title, booktitle, year | pages, doi |
| @book | author/editor, title, publisher, year | isbn, doi |
| @misc | author, title, year | doi or url |
Any `@article` entry missing `volume`, `pages`, or `doi` is considered **incomplete** and must be enriched.
#### Step 2: Web Search for Missing Metadata
For each incomplete entry, use the **parallel-web skill** to search for the missing information:
**Option A — Search by title and author** (best for finding DOI):
```bash
parallel-cli search "FIRST_AUTHOR TITLE JOURNAL_NAME volume pages DOI" \
--json --max-results 10 \
-o sources/search_citation_CITATIONKEY.json
```
**Option B — Extract from DOI page** (best when DOI is known but volume/pages missing):
**Validation Checks** (see `references/citation_validation.md`):
1. **DOI Verification**:
- DOI resolves correctly via doi.org
- Metadata matches between BibTeX and CrossRef
- No broken or invalid DOIs
2. **Required Fields**:
- All required fields present for entry type
- No empty or missing critical information
- Author names properly formatted
3. **Data Consistency**:
- Year is valid (4 digits, reasonable range)
- Volume/number are numeric
- Pages formatted correctly (e.g., 123--145)
- URLs are accessible
4. **Duplicate Detection**:
- Same DOI used multiple times
- Similar titles (possible duplicates)
- Same author/year/title combinations
5. **Format Compliance**:
- Valid BibTeX syntax
- Proper bracing and quoting
- Citation keys are unique
- Special characters handled correctly
**Validation Output**:
```json
{
"total_entries": 150,
"valid_entries": 145,
"errors": [
{
"citation_key": "Smith2023",
"error_type": "missing_field",
"field": "journal",
"severity": "high"
},
{
"citation_key": "Jones2022",
"error_type": "invalid_doi",
"doi": "10.1234/broken",
"severity": "high"
}
],
"warnings": [
{
"citation_key": "Brown2021",
"warning_type": "possible_duplicate",
"duplicate_of": "Brown2021a",
"severity": "medium"
}
]
}
```
#### Citation Count Standards by Venue
**Citations must always be high in number based on standards for journal and conference publications in the venue of choice or recommendation.** Never settle for a sparse reference list; establish an authoritative, rich context with dense, verified citations.
| Comprehensive literature reviews / market research reports | **40-65+** |
| Medical journals (NEJM, Lancet, JAMA) | **30-45+** |
Always adjust the citation target upward depending on standard density and practices of the target venue. Avoid 'lazy' citation over-repetition — do not repeatedly cite the same 1 or 2 papers to support multiple unrelated claims; draw from a diverse, high-quality set of reputable references.
Enforce these standards programmatically with `validate_citations.py --venue <venue>` or `--min-count <N>`.
Once the entire scientific report or paper has been drafted and written, perform a comprehensive post-writing verification of all citations before compiling the final deliverables:
1. **Verify No Missing or Unresolved Citations**: Check the draft or compiled document to ensure that every in-text citation correctly resolves to a reference in `references.bib`. There must be ZERO broken citation keys, missing identifiers, or unresolved references (e.g., `[?]` or `[citation needed]`).
2. **Verify No Unused (Dangling) Bibliography Entries**: Check that every entry in `references.bib` is actually cited in the body of the report. Remove any unused entries to keep the bibliography perfectly clean.
3. **Verify Citation Quantity Against Target Standards**: Ensure the final citation count meets or exceeds the high standard of the chosen or recommended venue (see table above). If the count is below standard, perform additional literature search first, find high-quality papers, and integrate them into appropriate sections.
4. **Verify Metadata Completeness**: Confirm that all cited entries contain complete, fully-verified fields (all author names, complete journal/conference names, exact year, volume, issue, page range, and valid DOI).
# Batch processing (file with one identifier per line)
python scripts/extract_metadata.py \
--input paper_ids.txt \
--output references.bib
# Different output formats
python scripts/extract_metadata.py \
--doi 10.1038/nature12345 \
--format json # or bibtex, yaml
```
### validate_citations.py
Validate BibTeX entries for accuracy, completeness, citation count standard compliance, and manuscript integration.
**Features**:
- DOI verification via doi.org and CrossRef
- Required field checking
- Duplicate detection
- Format validation
- **Publication standard citation count checks** against specified venues (Nature, NeurIPS, review, etc.) or custom thresholds.
- **Mandatory post-writing checks** matching manuscript citations (Markdown or LaTeX) with defined BibTeX entries to detect unresolved/missing or unused references.
- **Solution**: Run Phase 2.5 metadata enrichment — web search for every missing field before proceeding. NEVER leave an @article entry without volume, pages, and DOI.
7. **Outdated preprints**: Citing preprint when published version exists
- **Solution**: Check if preprints have been published, update to journal version
8. **Special character issues**: Broken LaTeX compilation due to characters
- **Solution**: Use proper escaping or Unicode in BibTeX
9. **No validation before submission**: Submitting with citation errors
- **Solution**: Always run validation as final check
10. **Manual BibTeX entry**: Typing entries by hand
- **Solution**: Always extract from metadata sources using scripts
## Example Workflows
### Example 1: Building a Bibliography for a Paper
