Inputs

The tool requires a path to a ro-crate (directory) passed in --inputdir parameter as its input. The directory should contain following files:

  • blue, red, green, yellow:

    Directories containing downloaded images in different color spectrum.

  • 1_image_gene_node_attributes.tsv:

    A TSV file containing attributes for image genes generated during the first fold of execution. 2_image_gene_node_attributes.tsv corresponds to the second fold of execution etc.

    It is necessary that the file contains name and filename columns as they are directly referenced in the code, but it will usually also have other columns described below:

    • name - contains the gene symbol. In some cases, it can contain an ensembl ID or another query, that mygene was queried with.

    • represents - a comma-separated list of Ensembl gene IDs that the gene symbol represents.

    • ambiguous - a comma-separated list of gene symbols/ queries that are considered ambiguous for the given antibody.

    • antibody - the ID of the antibody used in the experiment.

    • filename - the filename where the image associated with the gene and antibody can be found.

    • imageurl - the url of the image if found

name        represents      ambiguous       antibody        filename        imageurl
UHRF2       ensembl:ENSG00000147854         HPA026633       B2AI_1_untreated_D2_R5_ no image url found
TET3        ensembl:ENSG00000187605         HPA050845       B2AI_1_untreated_E5_R5_ no image url found
HDAC6       ensembl:ENSG00000094631         HPA003714       B2AI_1_untreated_G3_R5_ no image url found
HDAC3       ensembl:ENSG00000171720         HPA052052       B2AI_1_untreated_D3_R7_ no image url found
  • 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. c. Images: details about specific image files, including keywords, descriptions, formats, and content URLs.