MeSH Tables

puremoe ships three MeSH reference tables: a thesaurus of descriptors and entry terms, a tree of hierarchical classifications, and a bundled table of MeSH annotation counts per descriptor across PubMed.

library(puremoe)
library(dplyr)
library(DT)

MeSH thesaurus

data_mesh_thesaurus() downloads and combines the MeSH Descriptor Thesaurus and Supplementary Concept Records (SCR). One row per term, including synonyms and entry terms for each descriptor.

thesaurus <- puremoe::data_mesh_thesaurus()

thesaurus |>
  head(20) |>
  DT::datatable(rownames = FALSE, options = list(scrollX = TRUE))

MeSH trees

data_mesh_trees() provides the hierarchical classification structure. Each descriptor can appear in multiple branches; tree_location encodes the full path (e.g., I01.880.604 = Social Sciences > Political Science > Political Systems).

trees <- puremoe::data_mesh_trees()

trees |>
  head(20) |>
  DT::datatable(rownames = FALSE, options = list(scrollX = TRUE))

MeSH descriptor frequencies

data_mesh_frequencies is a bundled dataset giving the annotation frequency of each MeSH descriptor across the full PubMed corpus (39.7 M PMIDs, April 2026). Counts reflect the number of records indexed with each descriptor by NLM curators, not text frequency, making them suitable as a baseline for enrichment analyses against arbitrary PubMed subsets.

puremoe::data_mesh_frequencies |>
  head(20) |>
  dplyr::mutate(prop_total = round(prop_total, 4)) |>
  DT::datatable(rownames = FALSE, options = list(scrollX = TRUE))

Persistent storage

The downloaded MeSH thesaurus and tree tables are fetched from GitHub on each call by default. To avoid re-downloading every session, set use_persistent_storage = TRUE; the files are cached to a system data directory and reused on subsequent calls. data_mesh_frequencies is bundled with the package and does not need to be downloaded.

thesaurus <- puremoe::data_mesh_thesaurus(use_persistent_storage = TRUE)
trees     <- puremoe::data_mesh_trees(use_persistent_storage = TRUE)