Orphanet Explorer

A Python package for processing and merging Orphanet XML data files. This package provides tools to extract, transform, and combine data from various Orphanet XML files into a unified dataset.

Features

• Process multiple Orphanet XML file types
• Extract phenotype, functional consequences, natural history, and epidemiological data
• Merge datasets with intelligent handling of common columns
• Type-safe operations with comprehensive error handling
• Configurable output formats and locations

Installation

pip install orphanet_explorer

You can download data from https://www.orphadata.com/orphanet-scientific-knowledge-files/

Quick Start

from orphanet_explorer import OrphanetDataManager

# Initialize processor
processor = OrphanetDataManager(output_dir="output")

# Define input files
xml_files = {
    "phenotype": "data/en_phenotype.xml",
    "consequences": "data/en_funct_consequences.xml",
    "natural_history": "data/en_nat_hist_ages.xml",
    "references": "data/references.xml",
    "epidemiology": "data/en_epidimiology_prev.xml"
}

# Process files and save merged dataset
merged_data = processor.process_files(
    xml_files,
    output_file="merged_orphanet_data.csv"
)

Use Cases

1. Medical Research

   • Analyze disease phenotypes and their frequencies
   • Study disease inheritance patterns
   • Investigate prevalence across different populations

2. Clinical Applications

   • Build reference databases for rare diseases
   • Support diagnostic systems
   • Track epidemiological patterns

3. Data Integration

   • Combine Orphanet data with other medical databases
   • Create comprehensive disease profiles
   • Support machine learning models for disease classification

Basic Usage

# Process a single file type
processor = OrphanetDataManager()
root = processor.parse_xml("phenotype.xml")
phenotype_data = processor.extract_phenotype_data(root)

# Merge multiple datasets
merged_data = processor.merge_datasets([df1, df2, df3])

Contributing

We welcome contributions!

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Orphanet for providing the source data
• The rare disease research community

Citation

If you use this package in your research, please cite:

@software{orphanet_processor,
  author = A. Tinakoua,
  title = {Orphanet Explorer: A Python Package for Processing Orphanet Data},
  year = {2025},
  url = {https://github.com/atinak/orphanet_explorer}
}