Pmparser and PMDB: resources for large-scale, open studies of the biomedical literature.
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ABSTRACT:
SUBMITTER: Schoenbachler JL
PROVIDER: S-EPMC7955988 | biostudies-literature | 2021
REPOSITORIES: biostudies-literature
Publications
pmparser and PMDB: resources for large-scale, open studies of the biomedical literature.
Schoenbachler Joshua L JL Hughey Jacob J JJ
PeerJ 20210311
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, pmparse ...[more]
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