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3.1 ACTION

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Xiaofeng Liao edited this page Sep 30, 2022 · 13 revisions

The NTR-ACTION (Netherlands Twin Register - Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies) with the goal to identify biomarkers for childhood aggression, is used as a demonstrator to demonstrate the pipeline from generation of ISA metadata file and importing of ISA metadata to the FDP, and some query examples to the FDP.

ACTION metadata

We capture the experimental metadata of the ACTION multi-omics data set (DNA methylation profiles, metabolomics) using the ISA metadata framework. An example of ACTION metadata captured in ISA metadata schema can be found on Github ^12.

ISA Generation

We developed a script (Jupyter notebook) that creates both ISA-Tab files and an ISA-JSON file with the metadata mentioned above. The notebook as well as a conda environment for running the notebook are available on GitHub ^13. A docker container to run this script can be found here ^14 .

Submit ISA

The script for importing the Investigation file to FDP can be found here ^15. A Docker container to run the importing script can be found here ^16.

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