Open matentzn opened 1 year ago
@matentzn terms merged is baked into the OWL API OBO parser to model alt_ids (parsing an OBO file containing alt_ids converts the alt_ids to obsolete terms with a replaced_by value of the main term, as well as an obsoletion reason of terms merged). I think this value should just be avoided completely if using OBO 1.2/1.4. 🫤 Maybe we can exclude alt_id from OBO 1.6.
Oh, and the reason I assume for the owl-axioms
header is that the obsolete terms that become alt_ids don't have a frame of their own in OBO, so no place to put their annotations.
@matentzn terms merged is baked into the OWL API OBO parser to model alt_ids (parsing an OBO file containing alt_ids converts the alt_ids to obsolete terms with a replaced_by value of the main term, as well as an obsoletion reason of terms merged). I think this value should just be avoided completely if using OBO 1.2/1.4. 🫤 Maybe we can exclude alt_id from OBO 1.6.
Really important to have a standard & well documented migration strategy for any existing alt_ids - given their long legacy. That was the point of the baked-in conversion.
Minimal ontology:
Save with OWLAPI 3.5.25:
Funnily this works:
Note the
property_value: IAO:0000231 somestring
This is a big problem for Mondo because I am trying to standardise all OBO ontologies to using obsolescence reasons correctly.