puremoe

CRAN version CRAN downloads

puremoe unifies access to PubMed and the NLM/NIH data stack behind one consistent, pipe-friendly interface: search PubMed, then pull abstracts, affiliations, citation metrics, entity annotations, full text, or MeSH resources. The same tabular outputs feed a small analysis layer – citation snowballing, network construction, sentence-mapped entity annotations, and co-occurrence – with PMIDs as the common currency from search through analysis.

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, 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
pubtations gene, disease, chemical, species, mutation annotations PubTator3
pmc_fulltext section-level open-access full text (requires URLs from pmid_to_ftp()) PMC Cloud Service

Analyze

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 an icites table into nodes + edges (within-corpus citations only), carrying RCR and clinical flags as node attributes; ready for igraph/tidygraph.
  • pubtator_sentences(pubtations) – map each PubTator3 entity annotation to the title/abstract sentence it occurs in, adding sentence_id, sentence, and sentence-relative offsets.
  • pubtator_cooccurrence(mapped, window, by, evidence) – count entity pairs co-occurring within or across sentences in pubtator_sentences() output; evidence = TRUE returns the supporting sentence context.

ID conversion

  • 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 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_mesh_frequencies – bundled PubMed-wide descriptor frequencies for enrichment-style baselines.

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