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TOP Data Import

Introduction

This GitHub repository contains the source code for a software component that integrates the Terminology- and Ontology-based Phenotyping (TOP) Framework into the LIFE-Adult-Study data request workflow. The primary goal of this component is to streamline the process of accessing and utilizing clinical research data within the study by providing a user-friendly interface for building computable phenotype models and improving data accessibility through standardized metadata.

Key Features

  • Computable Phenotype Modeling: Enables researchers to create and refine phenotype models using standardized terminologies, facilitating data exploration and analysis.
  • Metadata Standardization: Converts the study's existing metadata into a structured and machine-readable format, enhancing interoperability and mapping to external standards.
  • Data Request Streamlining: Simplifies the data request process by providing a more efficient and user-friendly approach.
  • Integration with the LIFE-Adult-Study: Seamlessly integrates with the existing study infrastructure to improve data accessibility and research efficiency.

Usage

When a LIFE project agreement is approved, a dataset is provided as a CSV file and associated metadata as a PDF. These files are used as input to the TOP data import component. The programmatic use of this component is described below.

  1. Create a copy of config.properties.dist and modify the file as needed (e.g., provide paths to CSV and PDF input files).
cp config.properties.dist config.properties
  1. Run care.smith.top.top_data_import.life.LIFEConverterApp.main and provide the configuration file as argument. Alternatively, you can call the converter the following way:
import care.smith.top.top_data_import.life.LIFEConverterApp;

public static void main(String[] args) {
  new LIFEConverterApp(new Config("config.properties")).convert();
}
  1. The resulting phenotype model, H2 database, and database adapter will be stored as specified in the configuration file.

Contribution and Development

Please see our Contributing Guide.

License

The code in this repository and the package care.smith.top:top-data-import are licensed under MIT.