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Preparing and merging a ROBOT template into Mondo

Updated 2025-06-10

Preparing and merging a ROBOT template into Mondo:

0:00:00 - 0:01:37 Intro and resources

0:01:38 - 0:23:59 preparing ROBOT template (simple example)

0:24:00 - 0:34:10 merging ROBOT template

0:34:11 - 0:42:00 preparing ROBOT template (extended example)

0:48:44 - 0:51:34 examples of error

0:56:42 - 1:05:22 preparing ROBOT template (examples for axioms)

  1. Create Google sheet with ROBOT template. See example Mondo ROBOT templates here. See more details about ROBOT templates here.
  2. Click File->Share->Publish to the Web
  3. Publish the specific sheet as TSV
  4. Copy the link to the TSV
  5. In the Terminal, navigate to the folder where the Mondo ontology is (usually in Documents/GitHub/mondo/src/ontology)
  6. Run git checkout master — mondo-edit.obo to revert mondo-edit.obo to the state it is on the master branch. This is only important if you have run the template command before.
  7. Run sh run.sh make TEMPLATE_URL="https://docs.google.com/spreadsheets/d/e/2PACX-1vQ_G0rImuYa8o72cgQ97bH7xIq_V4TF6YfHkQaQY7HJUElcolO2RSh4bE7d50HTlSL1Vq7LoRJSkKBD/pub?gid=875350397&single=true&output=tsv" merge_template -B (the TEMPLATE_URL should be your template link you have copied)
  8. Note - If you just want to module a tsv you have edited locally, place it somewhere into the src directory and run: sh run.sh make merge_template MERGE_TEMPLATE="modules/name_of_your_template.tsv"
  9. If all went well, mondo-edit.obo will be updated with the template.
  10. Branch + pull request
  11. As always, carefully review the diff before committing.

Recompile the template:

  1. Check out the current mondo-edit from master: git checkout master -- mondo-edit.obo
  2. In terminal: sh run.sh merge_template -B