biomed-enriched 0.1.0

Populate text paragraphs into PubMed sample datasets using a pre-built PMC XML index.

BioMed-Enriched

Populate paragraph text into BioMed-Enriched Non-Commercial split.

Install

pip install biomed-enriched

Requires Python ≥ 3.10. No extra setup needed for end-users.

Quick start (Python)

from biomed_enriched import populate

DATASET_DIR = "/path/to/biomed-enriched"  # input dataset
PMC_XML_ROOT = "/path/to/pmc/xml"          # PMC XML dump
OUTPUT_DIR = "/path/to/populated-biomed-enriched"  # drop arg to overwrite in-place

populate(DATASET_DIR, PMC_XML_ROOT, output_path=OUTPUT_DIR, splits="non-comm", num_proc=1)

The call overwrites the dataset in-place, adding a new text column as the third column (after article_id, path).

Quick start (CLI)

biomed-enriched \
  --input pubmed_sample \
  --xml-root /path/to/pmc/xml/root \
  --num-proc 8

Add --output DIR if you prefer writing to a new directory instead of overwriting.