puremoe provides a single, PMID-centered interface to PubMed and the wider NIH/NLM data stack — NIH iCite, PubTator3, and PMC. A PubMed search resolves to a set of PMIDs, which one retrieval function uses to assemble data frames from each service: metadata and abstracts, citation data, entity annotations, or full text. A local analysis layer then operates on those tables with no further API calls: corpus expansion and citation networks from iCite links, sentence-anchored PubTator co-occurrence and relation evidence, and MeSH descriptor keyness against PubMed-wide frequencies.
From CRAN:
install.packages("puremoe")Development version:
remotes::install_github("jaytimm/puremoe")search_pubmed(query, ...)-- PubMed query string → character vector of PMIDs. Accepts standard PubMed syntax: field tags ([TiAb],[MeSH Terms],[DP]), Boolean operators, wildcards.
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, publication type, MeSH terms | PubMed E-utilities |
pubmed_affiliations |
author × affiliation rows | PubMed E-utilities |
icites |
citation count, RCR, NIH percentile, field rate, clinical flags, citation links | NIH iCite |
pubtator |
gene, disease, chemical, species, mutation, and relation annotations (pubtations is accepted as a legacy alias) |
PubTator3 |
pmc_fulltext |
section-level open-access full text (requires URLs from pmid_to_ftp()) |
PMC Cloud Service |
Functions that transform already-retrieved tables -- no additional API calls.
citation_snowball(icites, direction, min_links, max_nodes)-- expand a corpus one hop along iCite citation links; returns a ranked candidate table with audit columns (seed,cited_links,citing_links,link_count).citation_network(icites)-- convert anicitestable intonodes+edges(within-corpus citations only), carrying RCR and clinical flags as node attributes; ready forigraph/tidygraph.pubtator_context(pubtator)-- add sentence IDs, sentence-relative entity spans, relation entity labels, relation sentence anchors, and a sentence lookup table to PubTator output.pubtator_cooccurrence(ctx, window, by)-- count entity pairs co-occurring within or across sentences in apubtator_context()result.pubtator_network(ctx)-- convert PubTator relations intonodes,edges, and leanevidencetables for graph workflows and edge inspection.mesh_keyness(records, measure)-- score a corpus's MeSH descriptors against PubMed-wide frequencies (log-odds or Dunning G2) to surface over- and under-represented terms.
pmid_to_pmc(pmids, ...)-- PMID → PMC ID + DOI via the NCBI ID Converter.pmid_to_ftp(pmids, ...)-- PMID → PMC ID + open-access PMC Cloud Service XML URL; pass URLs toget_records(endpoint = "pmc_fulltext").
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_mesh_frequencies-- bundled PubMed-wide descriptor frequencies for MeSH keyness baselines.
endpoint_info(endpoint)-- column definitions, rate limits, and notes for each endpoint. Returns a list or JSON; useful for tool schemas in LLM applications.
- Getting started --
search_pubmed()+ allget_records()endpoints end-to-end - MeSH tables -- thesaurus lookup, tree navigation, and PubMed-wide descriptor frequencies
- Citation snowballing -- expand a seed corpus along citation links, audit why each paper was admitted, and quantify the expansion space against PubMed-wide MeSH keyness
- PubTator context and relation networks -- add sentence context to PubTator annotations, count entity co-occurrence, and inspect relation-network evidence
MIT © Jason Timm
citation("puremoe")Report bugs or request features at https://github.com/jaytimm/puremoe/issues