Taxonomic Ranks

Developing an Ontology for Taxonomic Ranks

When the Teleost Taxonomy Ontology (TTO) was submitted to OBO, the suggest was made that the terms for taxonomic ranks (e.g., Family, Genus, Species) should be broken out. Originally these terms were included in the TTO and cross referenced to similar terms in the NCBI taxonomy ontology. Constructing an initial version of the ontology is straightforward, but there are some semantic issues that this page is devoted to.

The primary issue is how to represent the ordering among level terms. There are two points of view:

1. A special relation exists between taxonomic ranks. It is certainly transitive and antisymmetric.
2. The relation is simply part_of.

In order to resolve whether the rank ordering relation is simply part_of, it may be necessary to clarify the property 'has_rank' which is used to relate a particular taxon to its rank. This diagram may clarify where these relations and properties fit in the taxonomic ontologies.

     Cyrinidae   -------------------->  Family
         ^             has_rank           ^
         |                                |
    is_a |                                | "rank ordering"
         |                                |
      Davario    -------------------->  Genus
         ^             has_rank           ^
         |                                |
    is_a |                                |  "rank ordering"
         |                                |
 Davario aequipinnatus -------------->  Species
                         has_rank

According to the documentation for the NCBI taxonomy ontology, which shares this structure, 'has_rank' is a metadata relation. As such, it does not have any meaning for a reasoner. The assertion that 'has_rank' is a metadata relation might be subject to revision.

The is_a hierarchy in the left-side column indicates that taxa are sets, a minority view among philosophers of biology. If taxa are individuals, the is_a hierarchy should be replaced by a part_of hierarchy. However, that does not require the 'rank ordering' relation for level terms to be part_of because has_rank is a metadata relation.

There is another property of the 'rank ordering' that may be called, by analogy with the rational numbers, density. The rational numbers are considered dense because between any two rational numbers a third rational number can be found. Likewise, within limits, between any two rank terms another term can be inserted: for example by using sub- and super- prefixes.