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Nicole Vasilevsky edited this page Jul 28, 2022 · 1 revision

Merging a ROBOT template into MAxO

By Nicole Vasilevsky, updated 2022-07-28

Merging a ROBOT template into Mondo:

Description

ROBOT can be used to add new terms or new annotations to terms via a spreadsheet format. You can add new terms (and annotations) to MAxO, or just add new annotations, like add new synonyms or definitions. Using this ROBOT workflow is very helpful if you need to add a lot of new terms or annotations at once. ROBOT encodes both the template and the data in the same TSV; after the table header, the second row basically encodes the entire template logic, and the data follows in table row 3.

Instructions

  1. Create Google sheet with ROBOT template. For example, see this spreadsheet. 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. Run git checkout master — maxo-edit.owl to revert maxo-edit.owl to the state it is on the master branch. This is only important if you have run the template command before.
  6. 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 URL in the quotes (after the equal sign) should be your template link you have copied)
  7. If all went well, maxo-edit.owl will be updated with the template.
  8. Create a branch and move changes to the branch.
  9. Open Protege and spot-check the changes. If everything looks okay, save as and save the file.
  10. As always, carefully review the diff before committing.
  11. Create a pull request.

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"

Recompile the template:

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