Individual-based taxonomy

Representing evolutionary lineages using ontological individuals has some modeling advantages, and may be more realistic, compared with using a simple class hierarchy. We described some of the rationale in these ICBO conference proceedings. For the purposes of the Phenoscape KB, this model supports specification of the semantics of particular phenotype annotations: the phenotype applies to all members of a clade, is observed for some members, or is applied to the ancestor of the members.

In the KB build process, the VTO taxon class hierarchy is translated into a relationship graph. For every class relationships such as:

Class: Ictaluridae
    SubClassOf: Siluriformes

Individuals with the same IDs (using OWL punning) are created with a relationship such as:

Individual: Ictaluridae
    Facts: subCladeOf Siluriformes

The properties used in the evolutionary lineage model are currently held in the Phenoscape KB vocabulary ontology (a holding place for KB-specific and preliminary terms). These include the inverse property pairs subCladeOf/containsClade (taxon to taxon) and memberOf/hasMember (organism to taxon/taxon to organism). subCladeOf is transitive, and also a member of a given taxon is inferred to be a member of all taxa containing that taxon (using a property chain).