Data templates

This document describes how you can use tmtk to read your filled in templates and write the data to tranSMART-ready files. The templates can be downloaded here.

Create study templates

Using the tmtk.toolbox.create_study_from_templates() function you can process any template you have filled in, and output the contents to a format that can be uploaded to tranSMART. It has the following parameters:

  • ID (Mandatory) Unique identifier of the study. This argument does not define the name of the study, that will be derived from Level 1 of the clinical data template tree sheet.
  • source_dir (Mandatory) Path to the folder in which the filled in templates are stored. Template files are not searched recursively, so all should be in the same folder.
  • output_dir Path to the folder where the tranSMART files should we written to. If the path doesn’t exist the required folder(s) will be created. Default: ./<STUDY_ID>_transmart_files
  • sec_req Determines whether it should be a public or private study. Use Y for private or N for public. Default: Y

It is important that your source_dir contains just one clinical data template, which is detected by having “clinical” somewhere in the file name (case insensitive). If the template with general study level metadata is present it should have “general study metadata” in its name (case insensitive). All high-dimensional templates are detected by content, so file names are not important, as long as the names don’t conflict with the templates described above.

Note: It is possible to run the function with only high-dimensional templates, but keep in mind that in that case the concept paths will have to be manually added to the subject-sample mapping files.

# Load the toolkit
import tmtk

# Read templates and write to tranSMART files
tmtk.toolbox.create_study_from_templates(ID='MY-TEMPLATE-STUDY',
                                         source_dir='./my_templates_folder/',
                                         sec_req='N')