puremoe

CRAN version CRAN downloads

puremoe is an R package that unifies access to PubMed and NLM data behind a single retrieval function. Search PubMed, then pull abstracts, citation metrics, named-entity annotations, full-text articles, or MeSH resources – all as plain data.table objects, all pipe-compatible, no juggling separate APIs or output formats.

Installation

From CRAN:

install.packages("puremoe")

Development version:

remotes::install_github("jaytimm/puremoe")

The puremoe API

  • search_pubmed(query, ...) – PubMed query string → character vector of PMIDs. Accepts standard PubMed syntax: field tags ([TiAb], [MeSH Terms], [DP]), Boolean operators, wildcards.

Retrieve

get_records(pmids, endpoint, cores, sleep, ncbi_key) – the single retrieval function. Pass PMIDs and name an endpoint; get back a data.table.

endpoint returns source
pubmed_abstracts title, abstract, journal, year, authors, MeSH terms PubMed E-utilities
pubmed_affiliations author × affiliation rows PubMed E-utilities
icites citation count, RCR, NIH percentile, field rate NIH iCite
pubtations gene, disease, chemical, species, mutation annotations PubTator3
pmc_fulltext full-text sections (requires URLs from pmid_to_ftp()) PMC Open Access

ID conversion

  • pmid_to_pmc(pmids, ...) – PMID → PMC ID + DOI via the NCBI ID Converter.
  • pmid_to_ftp(pmids, ...) – PMID → PMC ID + open-access FTP URL; pass URLs to get_records(endpoint = "pmc_fulltext").

MeSH reference data

  • data_mesh_thesaurus() – MeSH descriptor thesaurus + supplementary concept records; one row per term/synonym.
  • data_mesh_trees() – MeSH hierarchical tree structure; tree numbers encode the classification path.
  • data_pmc_list() – PMC open-access file list mapping PMC IDs to file paths and licenses.

Utilities

  • endpoint_info(endpoint) – column definitions, rate limits, and notes for each endpoint. Returns a list or JSON; useful for tool schemas in LLM applications.

Vignettes

License

MIT © Jason Timm

Citation 

citation("puremoe")

Issues

Report bugs or request features at https://github.com/jaytimm/puremoe/issues