The package provides a single interface for accessing a range of NLM/PubMed databases, including PubMed abstract records, iCite bibliometric data, PubTator 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 ontology 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.
You can download the development version from GitHub with:
devtools::install_github("jaytimm/pubmedtk")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 <- pubmedtk::search_pubmed('("political ideology"[TiAb])',
use_pub_years = F)
# pmids <- pubmedtk::search_pubmed('immunity',
# use_pub_years = T,
# start_year = 2022,
# end_year = 2024) pubmed <- pmids |>
pubmedtk::get_records(endpoint = 'pubmed_abstracts',
cores = 3,
sleep = 1)
affiliationss <- pmids |>
pubmedtk::get_records(endpoint = 'pubmed_affiliations',
cores = 3,
sleep = 0.5)
icites <- pmids |>
pubmedtk::get_records(endpoint = 'icites',
cores = 4,
sleep = 0.25)
pubtations <- pmids |>
pubmedtk::get_records(endpoint = 'pubtations')When the endpoint is PMC, the `get_records() function takes a vector of filepaths (from the PMC Open Access list) instead of PMIDs.
pmclist <- pubmedtk::data_pmc_list(force_install = F)
pmc_pmids <- pmclist[PMID %in% pmids]
pmc_fulltext <- pmc_pmids$fpath[1:20] |>
pubmedtk::get_records(endpoint = 'pmc_fulltext', cores = 2)