The AMR Interpretation Engine is a standalone software which can interpret AMR measurements using CLSI and EUCAST breakpoints. The system also includes resource files which can be used independently of the interpretation system by 3rd parties.
About this app
This software was created by the WHONET development team (https://whonet.org) to facilitate the interpretation of antibiotic measurements according to the various supported guidelines available for this purpose, and published by those groups (CLSI, EUCAST, etc.).
The system can be integrated with your project via the Interpretation Engine library, or it can be used directly with either the command line interface or interactive interface projects.
The interactive interface is designed primarily to allow you to exercise the various functions of the system, but it can also allow you to process an input file into an output file with the interpretations.
The command-line interface facilitates easy incorporation with a 3rd-party system since the developer does not need to know how to use the various library functions associated. With that said, the CLI project is very small, so it should serve as a window into how to accomplish the basic needs if direct library integration was preferred.
The breakpoints and other tables will be kept up-to-date over time (Interpretaion Engine\Resources), and are useful in their own right, even if the software implementation of the engine is not for your purposes. For example, there are several groups who only utilize our tables. This repository now serves as the official source for these WHONET-related resources.
To process a complete data file, the input file must use WHONET naming conventions for the data columns. Sample data and configuration files are also provided in the Interpretation Engine\Resources\ folder.
We also provide SQL queries which can demonstrate certain aspects of the system, but which are not used directly by the code here. We have chosen to implement these function as pure C# code to assist others if they choose to make their own implementations, and also to eliminate any dependence on a certain database technology. Because the application only uses C# with a recent .NET version, it should be possible to build the library code for many platforms.
WHONET is a free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance.
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