File size: 5,006 Bytes
9bb8e2b 9a73104 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 |
---
license: other
license_name: genereviews
license_link: https://www.ncbi.nlm.nih.gov/books/NBK138602/
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
dataset_info:
features:
- name: id
dtype: string
- name: ch_id
dtype: string
- name: keywords
list: string
- name: title
dtype: string
- name: authors
dtype: string
- name: abstract
dtype: string
- name: content
dtype: string
- name: references
list: string
- name: created_date
dtype: string
- name: updated_date
dtype: string
- name: revised_date
dtype: string
- name: journal
dtype: string
- name: source_url
dtype: string
- name: publication_types
list: string
splits:
- name: train
num_bytes: 57554171
num_examples: 929
download_size: 15286246
dataset_size: 57554171
language:
- en
tags:
- medical
- gene
- reviews
- medicine
pretty_name: 'GeneReviews '
size_categories:
- n<1K
task_categories:
- text-generation
---
# GeneReviews Dataset Extraction
This project extracts text and metadata from GeneReviews® chapters downloaded from NCBI Bookshelf and creates a structured dataset in Hugging Face format.
## Overview
GeneReviews® is an international point-of-care resource for clinicians, providing clinically relevant and medically actionable information for inherited conditions. This project processes the XML files from the GeneReviews database and creates a structured dataset suitable for machine learning and research applications.
### 📈 **Dataset Statistics:**
- **Total Records**: 929 GeneReviews chapters
- **Average Abstract Length**: 899.6 characters
- **Average Content Length**: 56,377.9 characters
- **Total References**: 13,683 references across all chapters
- **Average References per Chapter**: 14.7
- **Chapters with >100 references**: 12 chapters
- **Total Keywords**: 9,616
- **Unique Keywords**: 6,824
## Source Information
- **Source**: [GeneReviews® on NCBI Bookshelf](https://www.ncbi.nlm.nih.gov/books/NBK1116/)
- **Publisher**: University of Washington, Seattle
- **ISSN**: 2372-0697
- **Content Type**: Clinical reviews of genetic conditions
- **License**: Open access for noncommercial research purposes
## Dataset Structure
Each record in the dataset contains the following fields:
| Field | Type | Description |
|-------|------|-------------|
| `id` | string | Unique chapter identifier |
| `ch_id` | string | Chapter ID (as you renamed it) |
| `title` | string | Chapter title |
| `authors` | string | Comma-separated author names |
| `journal` | string | "GeneReviews®" |
| **`abstract`** | **string** | **Chapter abstract/summary only** |
| **`content`** | **string** | **Chapter body content only (excluding abstract)** |
| **`references`** | **array** | **Array of reference citations** |
| `keywords` | array | Keywords and terms |
| `source_url` | string | Link to GeneReviews resource |
| `publication_types` | array | ["Review", "Clinical Review"] |
| `created_date` | string | Creation date |
| `updated_date` | string | Last update date |
| `revised_date` | string | Revision date |
## Files
- `extract_genereviews.py`: Main extraction script
- `load_genereviews_dataset.py`: Script to load and demonstrate the dataset
- `requirements.txt`: Python dependencies
- `genereviews_dataset/`: Hugging Face dataset directory
- `genereviews_dataset.json`: JSON version of the dataset
## Installation
1. Install the required dependencies:
```bash
pip install -r requirements.txt
```
## Usage
```python
from datasets import load_from_disk
# Load the dataset
dataset = load_from_disk("genereviews_dataset")
# Access by chapter
record = dataset[0]
chapter_id = record['ch_id']
# Access separated content
abstract = record['abstract'] # Only the abstract
content = record['content'] # Only the body content
references = record['references'] # Array of reference citations
```
### Search for Specific Conditions
```python
# Search for cystic fibrosis
cf_records = dataset.filter(lambda x: "cystic fibrosis" in x['title'].lower())
# Search for cancer-related content
cancer_records = dataset.filter(lambda x: "cancer" in x['content'].lower())
```
### Analyze Publication Dates
```python
# Find recently updated chapters
recent_updates = dataset.filter(lambda x: "2024" in x['updated_date'])
```
### Extract Keywords
```python
# Get all unique keywords
all_keywords = set()
for record in dataset:
all_keywords.update(record['keywords'])
```
## Citation
When using this dataset, please cite:
```
GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2025.
Available from: https://www.ncbi.nlm.nih.gov/books/NBK1116/
```
## License
This dataset is derived from GeneReviews®, which is owned by the University of Washington.
Permission is granted to reproduce, distribute, and translate copies of content materials
for noncommercial research purposes only, provided that proper attribution is given. |