Datasets:

Milad96
/

BIOBERT

language:
  - en
license: other
pretty_name: BIOBERT — Microbiology OA Full-Text Corpus
dataset_type: text
task_categories:
  - fill-mask
tags:
  - microbiology
  - open-access
  - pmc
  - europe-pmc
  - fulltext
  - mlm
  - pretraining
  - biobert
  - english
size_categories:
  - unknown

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/…"
}