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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:

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, Supplementary Concept Terms, and Pharmacological Actions; it also includes descriptor-level word embeddings (Noh & Kavuluru 2021). 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)

When the endpoint is PMC, the get_records() function takes a vector of filepaths (from the PMC Open Access list) instead of PMIDs.

pmclist <- puremoe::data_pmc_list(use_persistent_storage = T)
pmc_pmids <- pmclist[PMID %in% pmids]

pmc_fulltext <- pmc_pmids$fpath[1:5] |> 
  puremoe::get_records(endpoint = 'pmc_fulltext', cores = 1)

Summary

Output Colname Description
pubmed_abstracts pmid PMID
pubmed_abstracts year Publication year
pubmed_abstracts journal Journal name
pubmed_abstracts articletitle Article title
pubmed_abstracts abstract Article abstract
pubmed_abstracts annotations Mesh/Chem/Keywords annotations
pubmed_affiliations pmid PMID
pubmed_affiliations Author Author name
pubmed_affiliations affiliation Author affiliation
pubtations pmid PMID
pubtations tiab Title or abstract
pubtations id Entity ID
pubtations entity Extracted entity
pubtations identifier Knowledge base link (KB link)
pubtations type Entity type
pubtations start Start position (char)
pubtations end End position (char)
pmc_fulltext pmid PMID
pmc_fulltext section Full text section
pmc_fulltext text Full text content
icites pmid PMID
icites is_research_article Research article indicator
icites nih_percentile NIH percentile rank
icites is_clinical Clinical article indicator
icites citation_count Citation count
icites ref_count Reference count
icites citation_net Citation network (to/from edgelist)