BIOBERT — Microbiology OA Full-Text Corpus

Purpose: Provide an English Open-Access–only full-text corpus in microbiology and related domains for:

• Domain/Task-Adaptive Pretraining (DAPT/TAPT) with Masked Language Modeling (MLM)
• Fine-tuning BERT-style models such as BioBERT

⚠️ Copyright / License: This repository includes OA items only (e.g., PMC / Europe PMC OA). Each item must be used under its original upstream license. The fields license_type and license_url are included in every record. This repository does not grant a new license for redistribution.

Data format

Recommended file format: JSON Lines (.jsonl) — one document/section per line.

Example record

{
  "id": "pmcid:PMC1234567#sec3",
  "title": "Sample article title",
  "text": "full body text …",
  "source": "PMC",
  "pmcid": "PMC1234567",
  "doi": "10.xxxx/xxxx",
  "year": 2024,
  "journal": "Journal Name",
  "section": "body",
  "license_type": "CC-BY-4.0",
  "license_url": "https://creativecommons.org/licenses/by/4.0/",
  "url": "https://europepmc.org/…"
}