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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, Supplementary Concept Terms, and Pharmacological Actions; it also includes descriptor-level word embeddings (Noh & Kavuluru 2021). Via the mesh-resources library.
Get the released version from CRAN:
Or the development version from GitHub with:
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) 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)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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