puremoe

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

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

Getting started – search_pubmed() + all get_records() endpoints end-to-end
MeSH-guided search – thesaurus lookup, tree navigation, and controlled-vocabulary queries

License

Citation

citation("puremoe")

Issues

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