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Outputs
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The tool creates several files and folders in the specified output directory.
Below is the list and description of each output generated by the tool.

Outputs
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- ``ppi_emd.tsv``:
    A TSV file that contains the embeddings for the protein-protein interactions (PPIs). The first column consists of gene names, followed by the embedding vectors in subsequent columns.

.. code-block::

            1	2	3	4
    HDAC2	0.00322267	0.068772331	0.087871492	0.074549779
    SMARCA4	0.014913903	-0.025018152	-0.01334604	-0.050020121
    DNMT3A	0.030166976	0.082494646	0.083659336	-0.005459526
    KDM6A	0.058055822	0.151974067	0.122265264	0.057505969
    RPS4X	0.016731756	0.046027087	0.041698962	0.010518731


Logs and Metadata
-----------------

- ``error.log``:
    Contains error logs generated during the execution of the script.

- ``output.log``:
    A log file detailing the standard messages, warnings, or any information generated during the execution.

- ``ro-crate-metadata.json``:
    Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.

    The main object contains identifier (@id), type (@type), name, descriptions, keywords and isPartOf, that describes the hierarchical relationship (organization and project).

    Graph: The @graph key contains an array of objects that detail other entities related to the main dataset.
    a. Metadata, Datasets, Software
    b. Output Files: details of output files generated by the tool.