citation-management

Run the doi_to_bibtex.py script with the DOI as an argument, and it queries the CrossRef content negotiation API to return a formatted BibTeX entry. It also supports batch conversion from a file containing one DOI per line.

Use search_pubmed.py with a query containing MeSH field tags, such as "Diabetes Mellitus, Type 2"[MeSH], combined with date ranges and publication type filters. Results export to JSON or directly to BibTeX via the NCBI E-utilities API.

DOI metadata comes primarily from the CrossRef API, which provides publisher-supplied fields like authors, title, journal, volume, and pages. PMIDs use PubMed E-utilities, and arXiv IDs use the arXiv API, with DataCite available for datasets.

Yes, validate_citations.py verifies each DOI resolves via doi.org and compares the CrossRef metadata against the BibTeX entry. It also checks required fields, detects duplicates, and can auto-fix common formatting issues.

Merging bibliographies from multiple searches often includes the same paper under different citation keys. Run format_bibtex.py with the --deduplicate flag to detect entries sharing the same DOI or similar titles and remove the extras.

Yes, extract_metadata.py accepts arXiv IDs and queries the arXiv API for title, authors, and abstract. If the preprint has been published with a DOI, it generates an @article entry; otherwise it creates an @misc entry marked as a preprint.