1. Taxonomic ontologies: Bridging phylogenetic and taxonomic history Peter Midford University of Kansas Phenoscape Project

2. Teleost Taxonomy Ontology (TTO) overview Use of TTO Taxa: Classes or individuals

3. TTO Overview Generated from the Catalog of Fishes (CoF) Latest TTO includes synonyms extracted from CoF’s free-text taxonomic status Includes database and URI cross references Additional properties, such as is_extinct Uses OBO format Structured like OBO rendering of NCBI taxonomy

4. TTO Overview (2) The TTO contains 36,197 terms: 30,534 species 5048 genera 542 families. 43,117 taxonomic (mostly species) synonyms Embedded rank ontology has 8 terms

5. TTO workflow TTO Update Catalog of Fishes TTO Manual commit TTO term request tracker Curators Teleost-discuss Mail list TTO administrator Area specialists update revision

6. How Phenoscape uses the TTO

7. …opercle shape… Davario davario …triangular… TaxaTaxa Characters............

8. Taxonomy Ontology Anatomy Ontology Qualities Ontology (PATO) Davario davarioopercle (shape)triangular Davario davario:opercle(shape)triangular Entity Quality

9. Taxa: From Classes to Individuals

10. Danio rerioDanioCyprinidae Cyprin i formes Actinopterygii SpeciesGenusFamilyOrderClass has_rank is_a Taxonomic_rank is_a (Current) TTO Design

11. Classes vs. Individuals Classes are sets of individuals, defined by shared properties Gold atom - any atom with 79 protons Ahistorical - don’t appear or go extinct Hierarchy uses is_a Occur in a bounded region of space or time Individuals are not necessarily compact or continuously connected –Genealogy links together individuals in a species Hierarchy uses part_of

12. Clades as Individuals Species Genus Family part_of A species contains fewer lineages and covers less time than its containing genus

13. Why individuals? The metaphysical argument Making rank terms more than annotations Inference support Bridging taxon concepts and phylogenies

14. Inference Support Classes/is_a Supports property inheritance Supports ‘classifiers’ (similar to diagnostic keys) Problem with character reversals Individuals/part_of Supports ‘bottom up’ reasoning, which better represents inference in phylogeny and taxonomy (generalizing from specimens to groups) Appropriate for properties such as geographic ranges

15. Bridging Clades and Taxon Concepts Clades are connected historical entities that appear and go extinct  Individual Taxon concepts are historical entities subject to events such as revision and demotion  Individual Why use a class to bridge entities best modeled as individuals?

16. Thanks to Stan, Paula, Hilmar, Todd, and Jim