Citation Management

• You are building or cleaning a bibliography for a manuscript, thesis, or literature review and need to convert DOIs, PMIDs, or arXiv IDs into properly formatted BibTeX entries in bulk.
• You need to search Google Scholar or PubMed programmatically — including filtering by date range, publication type, or MeSH terms — and export results directly to BibTeX.
• You have an existing BibTeX file that needs deduplication, formatting standardization, and DOI verification before submission.
• You are working in a LaTeX-based writing workflow and need validated, consistently formatted references that integrate with the literature-review or scientific-writing skills.

• You only need a single ad-hoc citation and can retrieve it manually from a publisher's site faster than setting up a workflow.
• Your project uses a citation style not based on BibTeX (e.g., footnote-only formats in some humanities journals) — this skill is oriented around BibTeX output.
• You need full-text retrieval or PDF management; this skill handles metadata and references only, not document storage.

Search Google Scholar and PubMed programmatically using search_google_scholar.py and search_pubmed.py. Supports advanced operators, MeSH terms, date range filters, publication type filters, sorting by citation count, and export to JSON or BibTeX.

Convert any combination of DOIs, PMIDs, arXiv IDs, or URLs to complete citation metadata using extract_metadata.py. Sources include CrossRef (DOIs), PubMed E-utilities (biomedical), arXiv API (preprints), and DataCite (datasets and software) — all free, no API key required for most.

Use doi_to_bibtex.py for fast single or batch DOI conversion. Accepts a list of DOIs from a file (one per line) and outputs a ready-to-use .bib file, with optional clipboard support for individual entries.

validate_citations.py checks DOI resolution via doi.org and CrossRef, verifies required fields per BibTeX entry type, detects duplicates, and validates syntax. An --auto-fix flag corrects common issues automatically and outputs a structured JSON validation report.

format_bibtex.py standardizes field order, indentation, author name format, and title capitalization; sorts entries by key, year, or author; and removes duplicate entries. Produces consistently formatted .bib files ready for LaTeX compilation.

The five-phase workflow — search, metadata extraction, BibTeX formatting, validation, and writing integration — is fully scriptable. Each phase has dedicated tooling and can be combined into a single pipeline from raw search queries to a validated final_references.bib.

Search Google Scholar and PubMed for topic-relevant papers, extract metadata from results, append specific papers by DOI, then run deduplication, formatting, and validation in sequence to produce a submission-ready .bib file for a LaTeX document.

Given a plain-text file of DOIs collected during reading, run doi_to_bibtex.py --input dois.txt --output references.bib to generate a complete BibTeX file in seconds, bypassing all manual entry.

Pass a messy, multi-source .bib file through format_bibtex.py for standardization and deduplication, then through validate_citations.py with --auto-fix to resolve broken DOIs, missing required fields, and syntax errors before final submission.

Use search_google_scholar.py with --sort-by citations to surface seminal and highly cited papers on a topic, then pipe the results through extract_metadata.py to immediately generate a BibTeX file of the most influential references.