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INCATools / ontology-development-kit

Bootstrap an OBO Library ontology
http://incatools.github.io/ontology-development-kit/
BSD 3-Clause "New" or "Revised" License
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Add option to include defined-by annotation in imports #929

Closed anitacaron closed 11 months ago

anitacaron commented 1 year ago

Fixes #796

There're two cases:

  1. When use_base_merging: true, the option is added when merging all mirrors, so then we can get properly where the terms come from.
  2. When use_base_merging not defined, the option is added during the release process.
gouttegd commented 1 year ago

Should this be user-configurable? Ticket #796 says “we should consider adding this by default to ODK” (emphasis mine), which suggests users should have the possibility of disabling it.

anitacaron commented 1 year ago

Can you clarify, @matentzn, please?

matentzn commented 1 year ago

This should be configurable at least on import_group level, because the file size will blow up massively with that feature, and we want to at least give some hope that it can be switched off for people for which size matters (github file size limits etc).

Also, what about the case that you are not using base merging, but want to use this feature when creating the full.owl release? Isnt this another case where we may want this (we could use the same flag from import_group.annotate_defined_by)?

anitacaron commented 1 year ago

Ok, I'll add the configuration for this.

anitacaron commented 12 months ago

@matentzn is ready for review again

matentzn commented 12 months ago

From now on for changes that affect the pipeline, we should have two independent reviews. To minimise mistakes..