Outputs

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.

  • 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.

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
  • samples.csv:

    When --samples was supplied, this is the CSV copy of the file passed on the command line. When the HPA workflow was triggered (neither --samples nor --cm4ai_table) this file is generated automatically before downloads begin.

  • samplescopy.csv:

    A CSV file generated from the in-memory sample list. It is emitted whenever the tool needed to synthesize samples (for example when --cm4ai_table was used or when samples were built from HPA).

filename    if_plate_id     position        sample  locations       antibody        ensembl_ids     gene_names
B2AI_1_untreated_C1_R1_     B2AI_1_untreated        C1      R1              CAB079904       ENSG00000187555
B2AI_1_untreated_C1_R2_     B2AI_1_untreated        C1      R2              CAB079904       ENSG00000187555
B2AI_1_untreated_C1_R3_     B2AI_1_untreated        C1      R3              CAB079904       ENSG00000187555
  • unique.csv:

    A CSV file that is a copy of the file passed in via --unique flag. This file is only created when the optional/legacy --unique input is provided.

  • uniquecopy.csv:

    A CSV file that is generated from data passed in via --cm4ai_table flag. This file will only be created if the flag is set.

antibody    ensembl_ids     gene_names      atlas_name      locations       n_location
CAB079904   ENSG00000187555         MDA-MB-468              0
CAB079921   ENSG00000186298         MDA-MB-468              0
CAB080425   ENSG00000108773         MDA-MB-468              0
  • blue, red, green, yellow:

    Directories containing downloaded images in different color spectrum.

  • proteinatlas.xml.gz:

    A gzipped XML file containing information fetched from the Human Protein Atlas. This file is only present when the automatic HPA workflow was executed.

  • README.txt:

    A short text file summarizing the tool version, description, and produced outputs. Generated for every run.

  • task_<timestamp>_start.json / task_<timestamp>_finish.json:

    Metadata files emitted by cellmaps_utils.logutils describing when the run started/finished, the CLI arguments, and whether the execution succeeded.

Logs and Metadata

  • image_gene_node_attributes.errors:

    Logs any errors encountered during the creation of image gene node attributes.

  • output.log:

    A standard log file recording events, errors, and other messages during the execution of the tool.

  • error.log:

    A specialized log file recording only error messages encountered during the execution of the tool.

  • 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.