| 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** | |
| ```json | |
| { | |
| "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/…" | |
| } | |