The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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

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.
Health stats visible at Monitor.