v1.2.1

Full Changelog: v1.2.0...v1.2.1

v1.0.0

PhenoQC v1.0.0 Release

Overview

PhenoQC is a comprehensive toolkit for quality control of phenotypic datasets, providing robust validation, standardization, and harmonization capabilities. This release marks our first stable version, offering a complete suite of tools for researchers working with phenotypic data.

Key Features

Data Validation & Schema Compliance

• JSON schema-based validation for ensuring data structure consistency
• Format validation for various input types (CSV, TSV, JSON)
• Automated checks for data type consistency and required fields

Ontology Integration & Mapping

• Support for multiple ontologies (HPO, DO, MPO)
• Fuzzy matching for term mapping with configurable thresholds
• Custom mapping capabilities for specialized terminology

Missing Data Management

• Multiple imputation strategies:
  • Basic: mean, median, mode
  • Advanced: KNN, MICE, SVD
• Configurable handling of missing values
• Quality metrics for imputation assessment

Batch Processing Capabilities

• Parallel processing of multiple files
• Support for various input formats
• Progress tracking and error handling

User Interface Options

• Command-line interface (CLI) for automation and scripting
• Streamlit-based GUI for interactive data exploration
• Comprehensive logging and error reporting

Reporting & Visualization

• Detailed QC reports in multiple formats
• Visual summaries of data quality metrics
• Export capabilities for downstream analysis

Installation

pip install phenoqc

Citation

If you use PhenoQC in your research, please cite:

@software{silva_phenoqc_2024,
  author       = {Silva, Jorge Miguel Ferreira},
  title        = {PhenoQC: Quality Control for Phenotypic Data},
  year         = 2024,
  publisher    = {Zenodo},
}

License

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

PhenoQC 0.1.0

Changelog

All notable changes to PhenoQC will be documented in this file.

[0.1.0] - 2024-10-18

Added

• Initial release of PhenoQC
• Data validation functionality:
  • Schema validation using JSON schema
  • Format compliance checks
  • Integrity verification
  • Duplicate record detection
  • Conflicting record identification
• Ontology mapping feature:
  • Support for multiple ontologies (HPO, DO, MPO)
  • Custom mapping support
  • Synonym resolution
• Missing data detection and imputation:
  • Multiple imputation strategies (mean, median, mode, KNN, MICE, SVD)
  • Option to flag records with missing data
• Batch processing capability:
  • Support for multiple file processing
  • Parallel execution
• Command-line interface (CLI)
• Streamlit-based graphical user interface (GUI)
• Reporting and visualization:
  • PDF and Markdown report generation
  • Visual summaries using Plotly
• Support for CSV, TSV, and JSON input files
• Recursive directory scanning option
• Comprehensive logging system
• YAML-based configuration for ontology mappings and imputation strategies

Changed

• Improved error handling and logging
• Updated documentation and examples

Fixed

• Resolved critical bugs related to data validation and ontology mapping