--- name: citation-management version: 2.0.0 description: "Comprehensive citation management for academic research: search databases, extract metadata, validate citations, generate formatted BibTeX entries." allowed-tools: [Read, Write, Edit, Bash, WebSearch, WebFetch] --- # Citation Management Systematic citation management throughout the research and writing workflow. Search academic databases (Google Scholar, PubMed), extract accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validate citation information, and generate properly formatted BibTeX entries. Critical for maintaining citation accuracy and ensuring reproducible research. <\/overview> ## Prerequisites **Install dependencies before using scripts:** ```bash pip install requests ``` **Available Scripts:** | Script | Purpose | Usage | |--------|---------|-------| | `doi_to_bibtex.py` | Convert DOIs to BibTeX | `python {baseDir}\/scripts\/doi_to_bibtex.py 10.1038\/s41586-021-03819-2` | | `extract_metadata.py` | Extract metadata from any identifier | `python {baseDir}\/scripts\/extract_metadata.py --doi 10.xxxx\/xxxxx` | | `validate_citations.py` | Validate BibTeX file | `python {baseDir}\/scripts\/validate_citations.py references.bib` | | `search_pubmed.py` | Search PubMed programmatically | `python {baseDir}\/scripts\/search_pubmed.py "query terms"` | | `search_google_scholar.py` | Search Google Scholar | `python {baseDir}\/scripts\/search_google_scholar.py "query"` | | `format_bibtex.py` | Clean and format BibTeX | `python {baseDir}\/scripts\/format_bibtex.py input.bib -o output.bib` | <\/setup> ## Trigger Conditions Use this skill when: - Searching for papers on Google Scholar or PubMed - Converting DOIs, PMIDs, or arXiv IDs to BibTeX - Extracting complete metadata for citations - Validating existing citations for accuracy - Cleaning and formatting BibTeX files - Building a bibliography for a manuscript - Checking for duplicate citations - Ensuring consistent citation formatting **For these tasks, use specialized skills instead:** | Task | Recommended Skill | |------|-------------------| | Systematic literature review methodology | `literature-review` | | Thematic synthesis of findings | `literature-review` | | Journal-specific manuscript formatting | `venue-templates` | | Statistical result selection for citation | `statistical-analysis` | <\/when_to_use> ## Decision Matrix For detailed decision trees on citation style selection, metadata source routing, and database selection by field, see: → `{baseDir}\/references\/decision_framework.md` **Quick Reference:** | Decision | Key Guidance | |----------|--------------| | Citation style | Match to venue type (biomedical→Vancouver, CS→IEEE, social sciences→APA) | | Metadata source | DOI→CrossRef, PMID→PubMed E-utilities, arXiv→arXiv API | | Database selection | Search ≥2 databases per domain for comprehensive coverage | <\/decision_framework> ## Workflow ### Stage 1: Paper Discovery **Progress Milestones:** - 25%: Target databases identified - 50%: Search query constructed - 75%: Searches executed and results exported - 100%: Duplicates identified, search documented **Objective:** Find relevant papers using academic search engines **Steps:** 1. Identify target databases based on research domain (see decision matrix) 2. Construct search query using field-specific syntax 3. Execute search with appropriate filters (date range, article type) 4. Export results to structured format (JSON\/BibTeX) 5. Document search strategy for reproducibility **Exit Criteria:** - [ ] Search query documented with date - [ ] ≥2 databases searched for comprehensive coverage - [ ] Results exported in machine-readable format - [ ] Duplicate papers across databases identified **Google Scholar Query Syntax:** ``` "exact phrase" # Exact matching author:lastname # Author search intitle:keyword # Title search source:journal # Journal filter -exclude # Exclusion 2020..2024 # Year range ``` **PubMed Query Syntax:** ``` "term"[MeSH] # MeSH controlled vocabulary "term"[Title] # Title field "term"[Author] # Author field AND\/OR\/NOT # Boolean operators 2020:2024[PDAT] # Publication date range ``` --- ### Stage 2: Metadata Extraction **Progress Milestones:** - 25%: Identifier types classified - 50%: Primary API sources queried - 75%: Required fields verified - 100%: Gaps filled, author names standardized **Objective:** Convert paper identifiers to complete, accurate metadata **Steps:** 1. Identify identifier type (DOI, PMID, arXiv ID, ISBN) 2. Query primary API source (see routing table) 3. Verify all required fields present 4. Fill gaps from secondary sources if needed 5. Standardize author name format (Last, First) **Exit Criteria:** - [ ] All required fields populated (see Required Fields table) - [ ] DOI verified as resolvable via doi.org - [ ] Author names in consistent format - [ ] Journal name standardized (not abbreviated inconsistently) **Required Fields by Entry Type:** | Field | @article | @inproceedings | @book | @misc (preprint) | |-------|----------|----------------|-------|------------------| | author | ✓ Required | ✓ Required | ✓ Required | ✓ Required | | title | ✓ Required | ✓ Required | ✓ Required | ✓ Required | | year | ✓ Required | ✓ Required | ✓ Required | ✓ Required | | journal | ✓ Required | — | — | — | | booktitle | — | ✓ Required | — | — | | publisher | — | — | ✓ Required | — | | doi | ✓ Recommended | ✓ Recommended | ○ Optional | ✓ Recommended | | volume | ✓ Recommended | — | — | — | | pages | ✓ Recommended | ✓ Recommended | — | — | | url | ○ Optional | ○ Optional | ○ Optional | ✓ Required | | eprint | — | — | — | ✓ Required (arXiv) | --- ### Stage 3: BibTeX Generation **Progress Milestones:** - 25%: Entry types selected - 50%: Citation keys generated - 75%: Required fields populated - 100%: Title case protection applied, entries complete **Objective:** Generate clean, properly formatted BibTeX entries **Steps:** 1. Select correct entry type (@article, @inproceedings, etc.) 2. Generate citation key: FirstAuthorYear + keyword (e.g., Smith2024crispr) 3. Populate all required fields 4. Add recommended fields (DOI, URL) 5. Apply title case protection for proper nouns **Exit Criteria:** - [ ] Entry type matches publication type - [ ] Citation key is unique and meaningful - [ ] All required fields present - [ ] DOI field included (if available) - [ ] Special characters properly escaped **Inline Validation (verify as you generate):** After generating each entry, immediately verify before proceeding: ```bash # Quick validation of single entry python {baseDir}\/scripts\/validate_citations.py entry.bib # Or validate DOI resolution manually curl -sI "https:\/\/doi.org\/10.xxxx\/xxxxx" | head -1 # Should return: HTTP\/2 302 or HTTP\/1.1 302 ``` Fix any errors before generating the next entry. This prevents error accumulation. **BibTeX Templates:** ```bibtex @article{AuthorYearkeyword, author = {Last1, First1 and Last2, First2}, title = {Article {Title} with {Proper Noun} Protection}, journal = {Journal Name}, year = {2024}, volume = {10}, number = {3}, pages = {123--145}, doi = {10.1234\/example}, } @inproceedings{AuthorYearkeyword, author = {Last, First}, title = {Paper Title}, booktitle = {Proceedings of Conference Name}, year = {2024}, pages = {1--10}, doi = {10.1234\/example}, } @misc{AuthorYearkeyword, author = {Last, First and Last2, First2}, title = {Preprint Title}, year = {2024}, eprint = {2401.12345}, eprinttype = {arXiv}, eprintclass = {cs.LG}, url = {https:\/\/arxiv.org\/abs\/2401.12345}, } ``` --- ### Stage 4: Validation **Progress Milestones:** - 25%: BibTeX syntax validated - 50%: Required fields checked - 75%: DOIs verified as resolvable - 100%: Duplicates removed, consistency verified **Objective:** Verify all citations are accurate and complete **Steps:** 1. Parse BibTeX file and check syntax 2. Verify required fields for each entry type 3. Validate DOIs resolve correctly 4. Detect duplicate entries (same DOI, similar titles) 5. Check for format consistency **Exit Criteria:** - [ ] Zero syntax errors in BibTeX file - [ ] 100% of entries have required fields - [ ] 100% of DOIs verified as resolvable - [ ] Zero duplicate entries - [ ] Consistent citation key format throughout **Validation Checklist:** | Check | Pass Criteria | Severity if Failed | |-------|---------------|-------------------| | DOI Resolution | doi.org returns 200 OK | High - fix immediately | | Required Fields | All present for entry type | High - incomplete citation | | Year Format | 4 digits, 1900-2030 | Medium - likely typo | | Page Format | num--num or single page | Low - cosmetic | | Unique Keys | No duplicates | High - LaTeX will fail | | Author Format | Last, First throughout | Medium - inconsistent | --- ### Stage 5: Integration **Progress Milestones:** - 25%: .bib file copied to manuscript directory - 50%: Bibliography command added to LaTeX - 75%: Document compiled, citations checked - 100%: Reference formatting verified against venue **Objective:** Integrate validated bibliography into manuscript workflow **Steps:** 1. Copy validated .bib file to manuscript directory 2. Add `\bibliography{filename}` to LaTeX document 3. Set citation style with `\bibliographystyle{}` 4. Compile document and check all `\cite{}` commands resolve 5. Verify reference formatting matches venue requirements **Exit Criteria:** - [ ] No undefined citation warnings in LaTeX log - [ ] Reference list renders completely - [ ] Citation style matches target venue - [ ] All citations appear in references (no orphans) <\/workflow> ## Success Criteria **Quantitative Thresholds:** | Metric | Minimum | Target | Excellent | |--------|---------|--------|-----------| | DOI resolution rate | 90% | 98% | 100% | | Required field completeness | 95% | 100% | 100% | | Duplicate detection | 90% caught | 98% caught | 100% | | Citation key uniqueness | 100% | 100% | 100% | | Author format consistency | 90% | 100% | 100% | **Completion Checklist:** - [ ] All entries have required fields for their type - [ ] 100% of DOIs verified as resolvable - [ ] Zero duplicate entries detected - [ ] Consistent citation key format (AuthorYearkeyword) - [ ] BibTeX file compiles without errors - [ ] Reference formatting matches target venue style <\/success_criteria> ## Scope **In Scope:** - Academic database searching (Google Scholar, PubMed, arXiv) - DOI\/PMID\/arXiv ID to BibTeX conversion - Citation metadata extraction and validation - BibTeX file formatting and deduplication - Citation style guidance for common venues - Preprint to published version updating **Out of Scope** (use specialized resources): - Systematic literature review methodology → use `literature-review` - Thematic synthesis of findings → use `literature-review` - Journal-specific manuscript formatting → use `venue-templates` - Reference manager software (Zotero, Mendeley, EndNote) tutorials → external resources - Citation network analysis → specialized bibliometric tools <\/scope> ## Common Pitfalls ### 1. Single Database Bias **Anti-pattern:** Only searching Google Scholar and missing field-specific databases. **Solution:** Search ≥2 databases per research domain. Use PubMed for biomedical, IEEE Xplore for engineering, arXiv for preprints. Document all searches for reproducibility. --- ### 2. Accepting Metadata Blindly **Anti-pattern:** ```bibtex % Accepting CrossRef output without verification @article{wrong2024, author = {Smith, J}, % Missing co-authors! title = {important study}, % Wrong capitalization year = {2023}, % Wrong year - published 2024 } ``` **Solution:** ```bibtex % Verified against original publication @article{Smith2024important, author = {Smith, John and Jones, Mary and Chen, Wei}, title = {An Important Study of {CRISPR} Applications}, year = {2024}, journal = {Nature Methods}, volume = {21}, pages = {100--115}, doi = {10.1038\/s41592-024-01234-5}, } ``` --- ### 3. Missing DOI Validation **Anti-pattern:** Including DOIs without verifying they resolve. **Solution:** Validate every DOI: `curl -sI https:\/\/doi.org\/10.xxxx\/xxxxx | head -1` should return 200 or 302. Remove or fix any non-resolving DOIs. --- ### 4. Inconsistent Citation Keys **Anti-pattern:** ```bibtex @article{ref1, ...} @article{SMITH2024, ...} @article{paper_about_crispr, ...} ``` **Solution:** ```bibtex @article{Smith2024crispr, ...} @article{Jones2023protein, ...} @article{Chen2024method, ...} ``` Use consistent format: FirstAuthorYearkeyword (e.g., Smith2024crispr). --- ### 5. Citing Outdated Preprints **Anti-pattern:** Citing arXiv preprint when peer-reviewed version is published. **Solution:** Before finalizing bibliography, check if any preprints have been published: 1. Search DOI registries for arXiv ID 2. Check preprint page for "published in" notice 3. Update entry to journal version with proper DOI --- ### 6. Duplicate Entries **Anti-pattern:** Same paper with different citation keys: ```bibtex @article{Smith2024a, doi = {10.1234\/example}, ...} @article{smithPaper, doi = {10.1234\/example}, ...} % Duplicate! ``` **Solution:** Deduplicate by DOI: Extract all DOIs, identify duplicates, keep entry with best metadata, remove others. --- ### 7. Manual BibTeX Entry **Anti-pattern:** Typing BibTeX entries by hand, introducing errors. **Solution:** Always extract from authoritative sources: - CrossRef API for DOIs - PubMed E-utilities for PMIDs - arXiv API for arXiv IDs Never type entries manually; copy-paste introduces errors. <\/anti_patterns> ## Output Templates For complete templates with examples, see: → `{baseDir}\/references\/output_templates.md` **Available Templates:** | Template | Used In | Purpose | |----------|---------|---------| | Search Strategy Documentation | Stage 1 | Document searches for reproducibility | | Validation Report (JSON) | Stage 4 | Machine-readable validation output | <\/templates> ## Related Skills | Skill | Relationship | |-------|-------------| | `literature-review` | Use for systematic search methodology; citation-management handles technical citation extraction | | `venue-templates` | Use for journal-specific formatting after citations are validated | | `scientific-writing` | Integrates validated bibliography into manuscript | | `research-lookup` | Use for quick fact-checking; citation-management for formal citations | **Skill Selection:** See `SKILL_ROUTER.md` for decision trees when multiple skills may apply. **Combined Workflow:** 1. `literature-review` → systematic multi-database search 2. `citation-management` → extract and validate all citations 3. `literature-review` → synthesize findings thematically 4. `citation-management` → verify final bibliography accuracy 5. `venue-templates` → format for target journal <\/cross_references> ## Reference Documents | Document | Purpose | |----------|---------| | `{baseDir}\/references\/decision_framework.md` | Citation style, metadata routing, database selection | | `{baseDir}\/references\/output_templates.md` | Search strategy and validation report templates | | `{baseDir}\/references\/google_scholar_search.md` | Complete Google Scholar search guide | | `{baseDir}\/references\/pubmed_search.md` | PubMed and E-utilities API documentation | | `{baseDir}\/references\/metadata_extraction.md` | Metadata sources and field requirements | | `{baseDir}\/references\/citation_validation.md` | Validation criteria and quality checks | | `{baseDir}\/references\/bibtex_formatting.md` | BibTeX entry types and formatting rules | ### External Resources **Search Engines:** - Google Scholar: https:\/\/scholar.google.com\/ - PubMed: https:\/\/pubmed.ncbi.nlm.nih.gov\/ - arXiv: https:\/\/arxiv.org\/ **Metadata APIs:** - CrossRef API: https:\/\/api.crossref.org\/ - PubMed E-utilities: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK25501\/ - arXiv API: https:\/\/arxiv.org\/help\/api\/ - DataCite API: https:\/\/api.datacite.org\/ **Tools:** - MeSH Browser: https:\/\/meshb.nlm.nih.gov\/search - DOI Resolver: https:\/\/doi.org\/ <\/references>