Support temporary IDs #3567
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Support temporary IDs #3567
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Add two ranges to the ID policy: * the "Temporary IDs" range (UBERON:99NNNNN), intended for automatically generated temporary IDs that must later be replaced by definitive IDs; * the "Automation" range (UBERON:12NNNNN), intended for all automated processes (e.g. KGCL, allocation of definitive IDs).
Add a helper rule in the custom Makefile to automatically replace temporary IDs in the -edit file by definitive IDs. Add a new GitHub Actions workflow to perform the ID replacement operation (1) whenever something is pushed to the master branch and (2) on demand on any other branch. This supports the two methods envisioned in #3564 for dealing with temporary IDs: (1) keep using temporary IDs throughout the life of a PR, and replace them on the master branch _after_ the PR has been merged; this happens entirely automatically; (2) use temporary IDs throughout most of the life of a PR, but replace them just before merging the PR; this has to be manually triggered by someone, ideally the same person who decides to merge the PR.
Add a new documentation file focusing on term ID management, and explaining how to use temporary IDs.
gouttegd
commented
Jun 20, 2025
| @@ -17,260 +16,269 @@ AnnotationProperty: allocatedto: | |||
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| AnnotationProperty: idprefix: | |||
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| AnnotationProperty: iddigits: | |||
| AnnotationProperty: iddigits: | |||
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Reviewers: all the changes in the uberon-idranges.owl files are due to the fact that the file has been re-serialized as a side-effect of the addition of the two new ranges. Those serialisation-induced changes are inconsequential.
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This PR implements the idea proposed in #3564 for allowing AI agents (or in fact any editor, AI or not) to use “temporary” term IDs that are later replaced by definitive IDs.
It allocates two new ID ranges:
Temporary IDsrange (UBERON:99NNNNN): any ID picked within that range is treated as a temporary ID, slated for later replacement by a definitive ID;Automationrange (UBERON:12NNNNN): this is a “normal” ID range (IDs picked within that range are not treated differently from any other ID), but is reserved for automated process – notably, for the process that replaces temporary IDs by definitive ones.It also adds a new GitHub Action workflow,
allocate-definitive-ids.yml, which finds all temporary IDs (all IDs in theUBERON:99NNNNNrange) in the -edit file and replaces them by newly allocated IDs from theAutomationrange. That workflow can be used in two different ways, corresponding to the two options outlined at the end of the #3564 ticket:(A) Manual trigger: When a PR contains temporary IDs, a Uberon maintainer should manually trigger the
allocate-definitive-ids.ymlworkflow on the PR’s underlying branch, just before merging the PR into the master branch. This will automatically add a commit to the PR, in which temporary IDs are replaced by definitive ones. The PR should then be merged as soon as possible once that commit has been added.(B) Automatic trigger: If a PR containing temporary IDs is merged into the master branch (with the temporary IDs still present), the
allocate-definitive-ids.ymlworkflow will automatically be triggered and push a new commit to replace the temporary IDs by definitive ones, directly on the master branch. This can act as a “fall-back” action to ensure that temporary IDs are never left in the master branch, in case a Uberon maintainer forgets to manually trigger the ID replacement workflow on a PR.