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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_typeandlicense_urlare 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/…"
}
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