For each intermediate node in ncbitaxon there is an implicit ancestral species/organism. Note the node itself represents a superclass that encompasses all instances of the node.
We can inject additional nodes, this is a SKETCH of how it might work
- Bilateria (NCBITaxon:33213)
- ancestral Bilateria (ID: NCBITaxon:33213_anc)
- descendants of ancestral Bilateria (ID: NCBITaxon:33213_desc)
- Protostome
- Deuterostome
- ....
The hierarchy would still be pairwise disjoint facilitating taxon checks, see geneontology/gaferencer#81
note: any other ID scheme could be used for the inject nodes
ancestral-X would have taxrank=species, but is an OWL class whose members are individual organisms (likely all dead, except for very recently speciated species) just like other classes in the ontology.
Note: a completely orthogonal discussion is the extent to which axioms can be injected into the direct database translation. This should not be discussed here. But the proposal here could be implemented as a separate optional bridge owl file.
For each intermediate node in ncbitaxon there is an implicit ancestral species/organism. Note the node itself represents a superclass that encompasses all instances of the node.
We can inject additional nodes, this is a SKETCH of how it might work
The hierarchy would still be pairwise disjoint facilitating taxon checks, see geneontology/gaferencer#81
note: any other ID scheme could be used for the inject nodes
ancestral-X would have taxrank=species, but is an OWL class whose members are individual organisms (likely all dead, except for very recently speciated species) just like other classes in the ontology.
Note: a completely orthogonal discussion is the extent to which axioms can be injected into the direct database translation. This should not be discussed here. But the proposal here could be implemented as a separate optional bridge owl file.