Description
Pubmed Unified REtrieval for Multi-Output Exploration.
Description
Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts, bibliometrics from 'iCite', pubtations from 'PubTator3', and full-text records from 'PMC'.
README.md
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 toget_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()+ allget_records()endpoints end-to-end - MeSH-guided search -- thesaurus lookup, tree navigation, and controlled-vocabulary queries
License
MIT © Jason Timm
Citation
citation("puremoe")
Issues
Report bugs or request features at https://github.com/jaytimm/puremoe/issues.