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How to run a uPheno 2 release

How to run a uPheno release

  1. cd src/ontology
  2. sh prepare_release.sh
  3. make public_release GHVERSION=v2025-07-21 (update the date to the current date)

uPheno 2 editors workflows

Prepare patterns for matching

This is the first step in the uPheno 2 release process. It prepares the patterns for matching by copying them to a specific directory.

cd src/ontology
make prepare_patterns_for_matching

Prepare changed patterns

Prepares the changed patterns by copying them to a specific directory. This process takes the original uPheno patterns curated by the uPheno team and prepares them for generating the final ontology. For example, this step ensures that pattern labels are updated and definitions as well.

cd src/ontology
make prepare_changed_patterns