Example file lists

The first line will be the File List’s header. The first column of the header has to be the word “Files”. Values for other header columns are not predefined except for annotations file list where also “Source Image”¹ column is mandatory. For the other columns we recommend using descriptive, self-explanatory names. Some examples of column names:

• For compound treatment experiments: Compound, Concentration, Time (Example File List)
• For genetic variation studies: Gene Identifier, Gene Symbol (Example File List)
• For antibody reagent studies: Antibody Name, Antibody ID, Target Protein Name, Target Protein ID (Example File List)
• For other high content screening studies: Plate, Well, Field (Example File List)
• Other commonly used annotations: Channel, Description, QC info (Example File List)
• For annotations: Source Image (mandatory), Annotation Type, Transformation, Creation Time (Example File List)

It is useful to include only attributes that have at least two distinct values for the set of image files you are describing in a particular file list; include values that are constant throughout the submission (e.g., “Organism” being “Homo Sapiens”) in the metadata of the study entered via the web form. You can use the Ontology Lookup Service to search and access different biomedical ontologies.

Each submission file should be listed in the file list, one per line. Use as many lines as there are files in your dataset, and enter the exact filenames in the first column. Please note that filenames are case-sensitive.

1. Source Image is the image which the annotation file annotates, e.g. a segmentation mask shows the segmentation of an image which is the source image. ↩︎