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 species5048 genera542 families.

43,117 taxonomic (mostly species) synonyms

Embedded rank ontology has 8 terms

TTO workflow

TTO UpdateCatalog of

Fishes TTO

Manual commit

TTO termrequest tracker

CuratorsTeleost-discuss

Mail listTTO administrator

Area specialists

update

revision

How Phenoscape uses the TTO

… opercle shape …

Davario davario … triangular …Taxa

Characters

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TaxonomyOntology

AnatomyOntology

QualitiesOntology(PATO)

Davario davario opercle (shape)triangular

Davario davario:opercle (shape)triangular

Entity Quality

Taxa: From Classes to Individuals

Danio rerio Danio Cyprinidae Cypriniformes Actinopterygii

Species Genus Family Order Class

has_rank has_rank has_rankhas_rank has_rank

is_a

is_ais_a

is_a is_a

Taxonomic_rank

is_ais_a

is_a

is_a

(Current) TTO Design

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

Clades as Individuals

Species

Genus

Family

part_of

part_of

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

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

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?

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