Skip to content
Tools for extracting and processing Pubmed and Pubmed Central records.
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.
man documentation edits and require rentrez Mar 6, 2014


Build Status

Tools for extracting and processing records from Pubmed and Pubmed Central.

This project is still very much in development... Please contact me with any questions, suggestions or bug reports.

I have built in support for searching and processing MeSH headings, making this package of particular use for biomedical researchers conducting systematic reviews and meta-analyses. Two of these functions (mesh_assoc_table and keyword_assoc_table) produce association matrices which can be fed into graph packages such as igraph to visualise the associations between different search terms.

Available functions:

  • fetch - Tools for bulk downloading of Pubmed records
    • fetch_in_chunks(ids, chunk_size = 500, delay = 0, ...)
    • pubmed_fetch(ids, file_format = "xml", as_r_object = TRUE, ...)
  • textsearch - Tools for text-mining of abstracts and metadata from downloaded records
    • get_articles_by_terms(corpus, term_list, where, case_sensitive = FALSE, ...)
    • record_counts_by_year(corpus)
  • io - saving records to disk and printing summaries of abstract lists to file or sdout
    • write_JSON_file(x, file)
    • write_record_list(articles, out_file = "", abstract_p = FALSE, markdown_p = FALSE, linestart = "* ")
  • locations - Geocoding functionality added for finding the coordinates of departments affiliated with Pubmed Articles.
    • geocode_addresses(addresses, sleeper = 0.33, depth = 3)
    • get_article_location_data(abstracts)
    • geocode_address(address, depth = 3)
  • mesh - Tools for processing and exploring associations between MeSH headings and other keywords
    • mesh_assoc_table(corpus)
    • keyword_assoc_table(corpus, keyword_list, keyword_names, ...)
    • get_mesh_headings(article)
    • mesh_heading_frequency(corpus)
You can’t perform that action at this time.