Do not "add OBO shorthands" to the RO mirror. #3359
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RO is currently mirrored in Uberon using a custom rule that bypasses the normal ODK mirroring rule to include an additional step, the addition of OBO shorthands to RO relations. "OBO shorthands" are basically a trick allowing to use, e.g. `part_of` instead of `BFO:0000050` in a class expression, as in: relationship: part_of UBERON:00000033 However there is no reason to forcefully inject OBO shorthands to all RO relations as we are currently doing. We can already create OBO shorthands as needed within uberon-edit, for the relationships that are actually used. For example, we already have this in uberon-edit: [Typedef] id: part_of name: part of xref: BFO:0000050 which creates the `part_of` shorthand for BFO:0000050. We should stick to doing that for the relations we are actually using, and stop injectinf fabricated shorthands for the entirety of RO. If people believe that all RO relations should have OBO shorthands, then they should ask the RO folks to add them at the source. It's not Uberon's job to do it. So this commit removes the rule that adds the OBO shorthands to the RO mirror, so that RO is now mirrored using the standard ODK-generated rule. closes #3016
cmungall
approved these changes
Oct 8, 2024
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RO is currently mirrored in Uberon using a custom rule that bypasses the normal ODK mirroring rule to include an additional step, the addition of OBO shorthands to RO relations.
"OBO shorthands" are basically a trick allowing to use, e.g.
part_ofinstead ofBFO:0000050in a class expression, as in:However there is no reason to forcefully inject OBO shorthands to all RO relations as we are currently doing. We can already create OBO shorthands as needed within uberon-edit, for the relationships that are actually used. For example, we already have this in uberon-edit:
which creates the
part_ofshorthand for BFO:0000050.We should stick to doing that for the relations we are actually using, and stop injectinf fabricated shorthands for the entirety of RO. If people believe that all RO relations should have OBO shorthands, then they should ask the RO folks to add them at the source. It's not Uberon's job to do it.
So this commit removes the rule that adds the OBO shorthands to the RO mirror, so that RO is now mirrored using the standard ODK-generated rule.
closes #3016