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.


  • 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.

        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.