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eliteportal / data-models

data models for the elite project
https://eliteportal.github.io/data-models/
MIT License
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Add TMT proteomics template - retry automation #61

Open avanlinden opened 1 month ago

avanlinden commented 1 month ago

Same as PR#48 but trying to get the updated workflows to run the data model conversion.

avanlinden commented 1 month ago

Looking at a test TMT assay metadata template, there is an issue where there's a column called tissue even though that's not specified in the template dependencies: https://docs.google.com/spreadsheets/d/1Zgmc3EY1z7PJ65ecOhDrqgEO57LUpLEbfLCBMVZVHzc/edit?gid=0#gid=0.

The issue appears to be that tissue is a valid value of the attribute specimenType in addition to being an attribute used as a manifest column, leaving us with a circular graph. I'm going to leave this for now so we can merge the template. Some options to deal with it in the future:

  1. rename the valid value to something like "tissue specimen", if there are no portal facets depending on that as annotation
  2. set up a component-based validation rule so the tissue column is NOT required in the TMT assay manifest and tell people to ignore it
  3. ?