NEWS.md
2026-06-23
get_records(endpoint = "pubtator") for PubTator3 output as a list of entities and relations tables. "pubtations" is accepted as a legacy alias.pubtator_context() to add sentence IDs, sentence-relative entity spans, relation entity labels, relation sentence anchors, and a sentence lookup table to PubTator output.pubtator_cooccurrence() to count entity co-occurrence directly from a pubtator_context() result or contextualized entity table. It is now a count-only helper over sentence windows; sentence evidence text is handled by joining to ctx$sentences when needed.pubtator_network() to convert PubTator relations into graph-ready nodes and edges tables plus a lean evidence table that maps edges back to relation rows and same-sentence support.citation_snowball() and citation_network() helpers for citation expansion and within-corpus citation-network construction.mesh_keyness() to score a corpus’s MeSH descriptors against PubMed-wide frequencies (log-odds or Dunning G2), identifying over- and under-represented terms for corpus characterization and search refinement.get_records(endpoint = "icites") includes citation-link list-columns where available and guards slow iCite batches with a timeout.get_records(endpoint = "pubtations") is retained as a legacy alias for endpoint = "pubtator".2026-04-21
data_mesh_frequencies, a bundled dataset of MeSH descriptor frequencies across the full PubMed corpus (39.7 M PMIDs, April 2026). Columns DescriptorUI, DescriptorName, n_pmids, and prop_total. Intended as a baseline for MeSH term enrichment analyses.pmid_to_ftp() updated to use the PMC Cloud Service on AWS S3 (pmc-oa-opendata.s3.amazonaws.com) in response to NCBI’s migration away from the legacy PMC FTP Service (transition period February-August 2026; FTP decommissioned August 2026). The function interface is unchanged.2026-01-26
pmid_to_ftp() to convert PMIDs to full-text download URLs for open-access PMC articles; pass $url to get_records(endpoint = 'pmc_fulltext').endpoint_info() to provide schema, columns, and rate limits for each endpoint.