NEWS

puremoe 1.1.0

2026-06-23

Added get_records(endpoint = "pubtator") for PubTator3 output as a list of entities and relations tables. "pubtations" is accepted as a legacy alias.
Added pubtator_context() to add sentence IDs, sentence-relative entity spans, relation entity labels, relation sentence anchors, and a sentence lookup table to PubTator output.
Updated 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.
Added 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.
Added citation_snowball() and citation_network() helpers for citation expansion and within-corpus citation-network construction.
Added 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".
Updated vignettes, README, and package description for the retrieval and local analysis workflow.

2026-04-21

Added 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

Fixed iCite API integration to handle changes in API response structure.
Removed modern pipe operators to maintain compatibility with R >= 3.5.
Improved error handling for Internet resource functions to comply with CRAN policy.

Added pmid_to_ftp() to convert PMIDs to full-text download URLs for open-access PMC articles; pass $url to get_records(endpoint = 'pmc_fulltext').
Added endpoint_info() to provide schema, columns, and rate limits for each endpoint.

Removed mesh descriptor embeddings functionality (data_mesh_embeddings() function).

2024-10-15

Fixed an issue with the internal function responsible for handling Pubtator3 data. This was due to changes in the data structures provided by Pubtator3 API. The function now correctly processes data retrieved via the updated biocjson format from the API endpoint.

2024-05-13

Fixed a typo that caused the full text retrieval to fail in the pmc_fulltext endpoint.