pmparser and PMDB: resources for large-scale, open studies of the biomedical literature

Joshua L. Schoenbachler and Jacob J. Hughey

bioRxiv

Abstract

Summary: PubMed is an invaluable resource for the biomedical community. Although PubMed is freely available, the existing API is not designed for large-scale analyses and the XML structure of the underlying data is inconvenient for complex queries. We developed an R package called pmparser to convert the data in PubMed to a relational database. Our implementation of the database, called PMDB, currently contains data on over 31 million PubMed Identifiers (PMIDs) and is updated regularly. Together, pmparser and PMDB can enable large-scale, reproducible, and transparent analyses of the biomedical literature.

Availability and implementation: pmparser is licensed under GPL-2 and available at https://pmparser.hugheylab.org. PMDB is stored in PostgreSQL and compressed dumps are available on Zenodo (https://doi.org/10.5281/zenodo.4008109).

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