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GeneReviews

Tasks:
Text Generation
Modalities:
Text
Formats:
parquet
Languages:
English
Size:
< 1K
Tags:
medical
gene
reviews
medicine
Libraries:
Datasets
pandas
License:
Dataset card Data Studio Files
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abstract
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a-mannosidosis
a-mannosidosis
[ "α-Mannosidosis", "a-Mannosidosis", "Lysosomal alpha-mannosidase", "MAN2B1", "Alpha-Mannosidosis" ]
Alpha-Mannosidosis
Can Ficicioglu, Karolina M Stepien
Summary The clinical phenotype of alpha-mannosidosis varies considerably, with a wide spectrum of clinical findings and broad variability in individual presentation. At least three clinical types have been suggested in untreated individuals: mild (clinically recognized after age ten years, with myopathy, slow progressi...
Mild form (type 1): typically recognized after age ten years, with myopathy, slow progression, and no skeletal abnormalities Moderate form (type 2): typically recognized before age ten years, with myopathy, slow progression, and presence of skeletal abnormalities Severe form (type 3): Obvious progression leading to e...
[]
11/10/2001
13/6/2024
18/7/2019
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
a-thal
a-thal
["Hemoglobin Bart Hydrops Fetalis (Hb Bart) Syndrome","Hemoglobin H (HbH) Disease","a-Thalassemia Tr(...TRUNCATED)
Alpha-Thalassemia
Hannah Tamary, Orly Dgany
"Summary Alpha-thalassemia (α-thalassemia) has two clinically significant forms: hemoglobin Bart hy(...TRUNCATED)
"For synonyms and outdated names see\n\nIn descending order of severity\n\n## Diagnosis\n\nAlpha-tha(...TRUNCATED)
[]
1/11/2005
1/10/2020
23/5/2024
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
aadc-def
aadc-def
["AADC Deficiency","AADC Deficiency","Aromatic-L-amino-acid decarboxylase","DDC","Aromatic L-Amino A(...TRUNCATED)
Aromatic L-Amino Acid Decarboxylase Deficiency
Nenad Blau, Toni S Pearson, Manju A Kurian, Sarah H Elsea
"Summary Individuals with aromatic L-amino acid decarboxylase (AADC) deficiency typically have compl(...TRUNCATED)
"## Diagnosis\n\nConsensus clinical diagnostic criteria for aromatic L-amino acid decarboxylase (AAD(...TRUNCATED)
[]
12/10/2023
23/1/2025
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
aars2-dis
aars2-dis
["AARS2-Related Infant-Onset Cardiomyopathy","AARS2-Related Neurodegeneration With or Without Leukoe(...TRUNCATED)
Tomasz Chmiela, Zbigniew K Wszolek
Summary The diagnosis of In In
"Infantile-onset cardiomyopathy\n\nNeurodegeneration with or without leukoencephalopathy\n\nFor othe(...TRUNCATED)
[]
31/10/2024
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
ab-lipo-p
ab-lipo-p
["Bassen-Kornzweig Syndrome","Bassen-Kornzweig Syndrome","Microsomal triglyceride transfer protein l(...TRUNCATED)
Abetalipoproteinemia
John R Burnett, Amanda J Hooper, Robert A Hegele
"Summary Abetalipoproteinemia typically presents in infancy with failure to thrive, diarrhea, vomiti(...TRUNCATED)
"## Diagnosis\n\nNo formal clinical diagnostic criteria for abetalipoproteinemia have been published(...TRUNCATED)
["S Bishara, S Merin, M Cooper, E Azizi, G Delpre, RJ Deckelbaum. Combined vitamin A and E therapy p(...TRUNCATED)
25/10/2018
19/5/2022
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
abs
abs
["POR Deficiency","PORD","POR Deficiency","PORD","Antley-Bixler Syndrome","Congenital Adrenal Hyperp(...TRUNCATED)
Cytochrome P450 Oxidoreductase Deficiency
Jan Idkowiak, Deborah Cragun, Robert J Hopkin, Wiebke Arlt
"Summary Cytochrome P450 oxidoreductase deficiency (PORD) is a disorder of steroidogenesis with a br(...TRUNCATED)
"Antley-Bixler syndrome\n\nCongenital adrenal hyperplasia due to apparent combined CYP17A1 and CYP21(...TRUNCATED)
["M Adachi, K Tachibana, Y Asakura, T Yamamoto, K Hanaki, A Oka. Compound heterozygous mutations of (...TRUNCATED)
8/9/2005
3/8/2017
2/11/2015
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
accpn
accpn
["Agenesis of Corpus Callosum with Peripheral Neuropathy (ACCPN)","Andermann Syndrome","Agenesis of (...TRUNCATED)
Hereditary Motor and Sensory Neuropathy with Agenesis of the Corpus Callosum
Claudie Gauvreau, Jean-Denis Brisson, Nicolas Dupré
"Summary Hereditary motor and sensory neuropathy with agenesis of the corpus callosum (HMSN/ACC), a (...TRUNCATED)
"## Diagnosis\n\nConsensus diagnostic criteria for hereditary motor and sensory neuropathy with agen(...TRUNCATED)
[]
2/2/2006
17/9/2020
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
achm
achm
["Complete Achromatopsia (Rod Monochromatism, Total Color Blindness)","Incomplete Achromatopsia","Co(...TRUNCATED)
Achromatopsia
Susanne Kohl, Herbert Jägle, Bernd Wissinger, Ditta Zobor
"Summary Achromatopsia is characterized by reduced visual acuity, pendular nystagmus, increased sens(...TRUNCATED)
"Complete achromatopsia (rod monochromatism, total color blindness)\n\nIncomplete achromatopsia\n\nF(...TRUNCATED)
[]
24/6/2004
20/9/2018
25/2/2016
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
achon1b
achon1b
["ACG1B, SLC26A2-Related Achondrogenesis","ACG1B","SLC26A2-Related Achondrogenesis","Sulfate transpo(...TRUNCATED)
Achondrogenesis Type 1B
Sheila Unger, Andrea Superti-Furga
"Summary Clinical features of achondrogenesis type 1B (ACG1B) include extremely short limbs with sho(...TRUNCATED)
"## Diagnosis\n\nAchondrogenesis type 1B (ACG1B) is a perinatal-lethal disorder with death occurring(...TRUNCATED)
[]
30/8/2002
9/6/2022
16/3/2023
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
achondroplasia
achondroplasia
["FGFR3-Related Achondroplasia","FGFR3-Related Achondroplasia","Fibroblast growth factor receptor 3"(...TRUNCATED)
Achondroplasia
Janet M Legare
"Summary Achondroplasia is the most common cause of disproportionate short stature. Affected individ(...TRUNCATED)
"## Diagnosis\n\nBoth the clinical and radiologic features of achondroplasia have been well defined (...TRUNCATED)
["MC Ain, JA Browne. Spinal arthrodesis with instrumentation for thoracolumbar kyphosis in pediatric(...TRUNCATED)
12/10/1998
6/8/2020
11/5/2023
GeneReviews®
https://www.ncbi.nlm.nih.gov/books/NBK1116/
[ "Review", "Clinical Review" ]
End of preview. Expand in Data Studio

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
  • 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:
pip install -r requirements.txt

Usage 

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 

# 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 

# Find recently updated chapters
recent_updates = dataset.filter(lambda x: "2024" in x['updated_date'])

Extract Keywords 

# 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.
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Size of downloaded dataset files:
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Size of the auto-converted Parquet files:
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Number of rows:
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