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

PeerJ

article

Joshua L. Schoenbachler¹  Jacob J. Hughey¹ 

[1]Department of Biomedical Informatics, Vanderbilt University Medical Center

[2]Department of Biological Sciences, Vanderbilt University

关键词: Publishing;    Pubmed;    Database;    Parsing;   

DOI  :  10.7717/peerj.11071

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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. pmparser is licensed under GPL-2 and available at https://pmparser.hugheylab.org. PMDB is available in both PostgreSQL (DOI 10.5281/zenodo.4008109) and Google BigQuery (https://console.cloud.google.com/bigquery?project=pmdb-bq&d=pmdb).

【 授权许可】

CC BY