Get Association Scores from the Open Targets Platform

Welcome! This is a small application to fetch the association scores for a given target or disease ID.

For any given target or disease ID this package allows you to:

1. Store into a JSON file the target-disease association information resulting from the query.
2. See a simple analysis of the scores indicating the maximum, minimum and average and standard deviation values of the overall association scores of each target or disease.

This package accesses the Open Targets Platform REST API data, more precisely from its association endpoint. You can see their documentation for more information.

Installation

Simply install it via:

git clone https://github.com/ireneisdoomed/otp_associations.git

from the source on GitHub.

Requirements

The package only requires the requests and numpy modules to access and process the data. The program has been tested with the versions indicated in the requirements file on Python version 3.8.3.

Usage

The command-line program admits two different parameters for analysis:

• -d: The ID of the disease for which you want to do the analysis. For example: EFO_0000384
• -t: The ID of the target for which you want to do the analysis. For example: ENSG00000167207

It also supports two other optional parameters:

• -e: Exports the result of the query to JSON format. You have to indicate the output filename.
• -m: Minimum score value to filter associations with a certain quality data point. Default is set to 0. Scores above 0.2 is a good trade-off

An example of the usage may be:

python main.py -d EFO_0000384 -m 0.2 -e EFO_0000384.json

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT