puremoe

PubMed Unified REtrieval for Multi-Output Exploration. An R package that provides a single interface for accessing a range of NLM/PubMed databases, including:

• PubMed abstract records,

• iCite bibliometric data,

• PubTator3 named entity annotations, and

• full-text entries from PubMed Central (PMC).

This unified interface simplifies the data retrieval process, allowing users to interact with multiple PubMed services/APIs/output formats through a single R function.

The package also includes MeSH thesaurus resources as simple data frames, including Descriptor Terms, Descriptor Tree Structures, and Supplementary Concept Terms. Via the mesh-resources library.

Installation

Get the released version from CRAN:

install.packages('puremoe')

Or the development version from GitHub with:

remotes::install_github("jaytimm/puremoe")

Usage

PubMed search

The package has two basic functions: search_pubmed and get_records. The former fetches PMIDs from the PubMed API based on user search; the latter scrapes PMID records from a user-specified PubMed endpoint – pubmed_abstracts, pubmed_affiliations, pubtations, icites, or pmc_fulltext.

Search syntax is the same as that implemented in standard PubMed search.

pmids <- puremoe::search_pubmed('("political ideology"[TiAb])',
                                 use_pub_years = F)

# pmids <- puremoe::search_pubmed('immunity', 
#                                  use_pub_years = T,
#                                  start_year = 2022,
#                                  end_year = 2024) 

Get record-level data

pubmed <- pmids |> 
  puremoe::get_records(endpoint = 'pubmed_abstracts', 
                       cores = 3, 
                       sleep = 1) 

affiliations <- pmids |> 
  puremoe::get_records(endpoint = 'pubmed_affiliations', 
                       cores = 1, 
                       sleep = 0.5)

icites <- pmids |>
  puremoe::get_records(endpoint = 'icites',
                       cores = 3,
                       sleep = 0.25)

pubtations <- pmids |> 
  puremoe::get_records(endpoint = 'pubtations',
                       cores = 2)

# For PMC full text, first convert PMIDs to PMC IDs
pmc_ids <- puremoe::pmid_to_pmc(pmids, sleep = 0.5)
pmc_fulltext <- pmc_ids$url[!is.na(pmc_ids$url)] |> 
  puremoe::get_records(endpoint = 'pmc_fulltext', 
                       cores = 1, 
                       sleep = 1)

For the pmc_fulltext endpoint, first use pmid_to_pmc() to convert PMIDs to PMC IDs and full URLs, then pass the url column to get_records().

Summary