# Alterlab Citation Mgmt > Manages citations for academic research — searches Google Scholar and PubMed for papers, extracts accurate metadata, validates citations, and generates properly formatted BibTeX entries. Use when finding papers, verifying citation information, converting DOIs to BibTeX, checking reference accuracy in scientific writing, or building a bibliography. Part of the AlterLab Academic Skills suite. - Skill: `alterlab-ieu/alterlab-citation-mgmt` (Agent Skill, multi-file: 18 files) - Install (CLI): `npx skillmds@latest add alterlab-ieu/alterlab-citation-mgmt` - Raw SKILL.md: https://api.skillmd.com/api/skills/alterlab-ieu/alterlab-citation-mgmt/raw - Safety review: pending (external: skill-scanner PASS, skillspector PASS) - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Research & Search - License: MIT - Author: AlterLab-IEU (https://skillmd.com/u/alterlab-ieu) - Updated: 2026-09-08 - Page: https://skillmd.com/skills/alterlab-ieu/alterlab-citation-mgmt --- # Citation Management ## Overview Manage citations systematically across the research and writing process: search academic databases (Google Scholar, PubMed), extract accurate metadata from multiple sources (CrossRef, PubMed, arXiv, DataCite), validate citation information, and generate properly formatted BibTeX. Critical for citation accuracy, avoiding reference errors, and reproducible research. Integrates with the `literature-review` skill. ## When to Use This Skill Use when: - Searching for specific papers on Google Scholar or PubMed - Converting DOIs, PMIDs, or arXiv IDs to properly formatted BibTeX - Extracting complete metadata (authors, title, journal, year, etc.) - Validating existing citations for accuracy or checking for duplicates - Cleaning, sorting, and formatting BibTeX files - Finding highly cited / seminal papers in a field - Building a bibliography for a manuscript or thesis ## Core Workflow Citation management is a five-phase pipeline. Each phase maps to a script (full CLI in `references/script_cli_reference.md`) and a deep-dive reference. ### Phase 1 — Paper discovery Search Google Scholar (broad, cross-discipline) and PubMed (biomedical, MeSH-indexed). ```bash python scripts/search_google_scholar.py "CRISPR gene editing" --limit 50 --output results.json python scripts/search_pubmed.py "Alzheimer's disease treatment" --limit 100 --output alz.json ``` Operators, MeSH/field tags, complex queries, and high-impact-paper heuristics: `references/search_strategy_reference.md`, `references/google_scholar_search.md`, `references/pubmed_search.md`. ### Phase 2 — Metadata extraction Convert any identifier (DOI, PMID, arXiv ID, URL) to complete metadata. CrossRef is the primary DOI source; PubMed E-utilities, arXiv, and DataCite cover the rest. ```bash python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2 # quick single DOI python scripts/extract_metadata.py --pmid 34265844 # any identifier type python scripts/extract_metadata.py --input identifiers.txt --output citations.bib # batch ``` Sources and extracted fields: `references/metadata_extraction.md` and the Metadata Sources section of `references/search_strategy_reference.md`. ### Phase 3 — BibTeX formatting Generate clean, standardized entries. Common types: `@article`, `@book`, `@inproceedings`, `@incollection`, `@phdthesis`, `@misc`. Protect title capitalization with `{}`, use `--` for page ranges, include a DOI for modern publications. ```bash python scripts/format_bibtex.py references.bib --deduplicate --sort year --descending \ --output clean_references.bib ``` Entry types, required fields, and formatting rules: `references/bibtex_formatting.md`. ### Phase 4 — Validation Verify required fields are present, data is consistent, and there are no duplicates. DOI resolution is network-bound and OFF by default — add `--check-dois` to actually hit doi.org/CrossRef (slow). `validate_citations.py` reports only; it does not rewrite the file. To apply fixes (page dashes, author separators, dedup), run `format_bibtex.py`. ```bash python scripts/validate_citations.py references.bib --check-dois \ --report validation.json --verbose ``` Validation criteria and report format: `references/citation_validation.md` and the Validation Checks summary in `references/search_strategy_reference.md`. ### Phase 5 — Integration with writing Export validated BibTeX into a LaTeX manuscript (`\bibliography{final_references}`). Pairs with `literature-review` (search/synthesis), `scientific-writing` (manuscript references), and `venue-templates` (style-specific formatting). End-to-end worked examples (build a bibliography, convert a DOI list, clean a messy `.bib`, find seminal papers): `references/example_workflows.md`. ## Best Practices **Search**: start broad then narrow; use multiple sources; leverage "Cited by" for seminal papers; document queries and dates. **Metadata**: prefer DOIs (most reliable, best CrossRef metadata); verify author names, venue, and year; handle preprints (use the published version when one exists); keep author-name and journal-abbreviation formatting consistent. **BibTeX quality**: meaningful citation keys (`FirstAuthor2024keyword`); protect title capitalization with `{}`; remove redundant fields; validate syntax regularly; organize per project and merge carefully to avoid duplicates. **Validation**: validate early and often; fix broken DOIs and missing fields promptly; manually review critical citations. ## Common Pitfalls 1. **Single-source bias** → search multiple databases. 2. **Accepting metadata blindly** → spot-check against originals. 3. **Ignoring DOI errors** → validate before submission. 4. **Inconsistent formatting** → standardize with `format_bibtex.py`. 5. **Duplicate entries** → use duplicate detection. 6. **Missing required fields** → validate for completeness. 7. **Outdated preprints** → update to the published version. 8. **Special-character issues** → escape or use Unicode in BibTeX. 9. **No final validation** → always run validation as the last check. 10. **Manual BibTeX entry** → always extract from metadata sources. ## Index of Bundled Resources ### References (`references/`) - `script_cli_reference.md` — full per-script features and CLI usage - `example_workflows.md` — four end-to-end worked workflows - `search_strategy_reference.md` — high-impact heuristics, Scholar operators, MeSH/field tags, metadata sources - `google_scholar_search.md` — complete Google Scholar search guide - `pubmed_search.md` — PubMed and E-utilities API documentation - `metadata_extraction.md` — metadata sources and field requirements - `citation_validation.md` — validation criteria and quality checks - `bibtex_formatting.md` — BibTeX entry types and formatting rules ### Scripts (`scripts/`) `search_google_scholar.py`, `search_pubmed.py`, `extract_metadata.py`, `validate_citations.py`, `format_bibtex.py`, `doi_to_bibtex.py`. ### Assets (`assets/`) `bibtex_template.bib` (example entries for all types), `citation_checklist.md` (QA checklist). ## External Resources - Google Scholar: https://scholar.google.com/ · PubMed: https://pubmed.ncbi.nlm.nih.gov/ - 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/ - MeSH Browser: https://meshb.nlm.nih.gov/search · DOI Resolver: https://doi.org/ ## Dependencies ```bash # Core pip install requests bibtexparser biopython # Optional: Google Scholar access, advanced validation, LaTeX char handling pip install scholarly selenium crossref-commons pylatexenc ``` ## Summary This skill provides search (Scholar + PubMed), automated metadata extraction (DOI/PMID/ arXiv/URL), citation validation (DOI verification + completeness), BibTeX formatting and cleaning, and quality assurance — all reproducible through documented search and extraction methods. Use it to maintain accurate, publication-ready bibliographies.