Taxonomic ontologies: Bridging phylogenetic and taxonomic history Peter Midford University of Kansas Phenoscape Project
Teleost Taxonomy Ontology (TTO) overview Use of TTO Taxa: Classes or individuals
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
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
TTO workflow Catalog of Fishes TTO Update TTO update Area specialists Manual commit revision Teleost-discuss Mail list TTO term request tracker TTO administrator Curators
Characters . . . Taxa . . .
Taxonomy Ontology Anatomy Ontology Qualities Ontology (PATO) (shape)triangular Davario davario opercle Davario davario:opercle (shape)triangular Quality Entity
(Current) TTO Design Taxonomic_rank is_a is_a is_a is_a is_a Species Genus Family Order Class has_rank has_rank has_rank has_rank has_rank is_a is_a is_a is_a Danio rerio Danio Cyprinidae Actinopterygii Cypriniformes
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 Classes vs. Individuals
Clades as Individuals Species part_of Genus part_of Family A species contains fewer lineages and covers less time thanits containing genus
Why individuals? The metaphysical argument Making rank terms more than annotations Inference support Bridging taxon concepts and phylogenies
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 Inference Support
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?