The Teleost Anatomy Ontology computable evolutionary morphology for

The Teleost Anatomy Ontology: computable evolutionary morphology for teleost fishes Wasila Dahdul University of South Dakota & National Evolutionary Synthesis Center John G. Lundberg Academy of Natural Sciences, Philadelphia

Dahdul, W. M. , Lundberg, J. G. , Midford, P. E. , Balhoff, J. P. , Lapp, H. , Vision, T. , Haendel, M. A. , Westerfield, M. and Mabee, P. M. 2010 In press. The Teleost Anatomy Ontology: Anatomical representation for the genomics age. Systematic Biology.

Teleost Anatomy Ontology: TAO • Domain of knowledge: teleost anatomy

Teleost Anatomy Ontology: TAO • Domain of knowledge: teleost anatomy • “Preferred” terms for anatomical structures (entities) and their definitions

Teleost Anatomy Ontology: TAO • Domain of knowledge: teleost anatomy • “Preferred” terms for anatomical structures (entities) and their definitions • Source of terms Zebrafish Anatomy + systematists who know fish taxa and morphological characters

Teleost Anatomy Ontology: TAO • Domain of knowledge: teleost anatomy • “Preferred” terms for anatomical structures (entities) and their definitions • Source of terms Zebrafish Anatomy + systematists who know fish taxa and morphological characters • Structures linked to one another by logically defined biological (anatomical & developmental) relationships

An example from the Teleost Anatomy Ontology endochondral bone is_a ventral hyoid arch basihyal cartilage part_of develops_from basihyal bone Photo: P. Mabee

Terms in the TAO term name: basihyal bone id: TAO: 0000316 def: "Endochondral bone that is the median and anteriorly projecting element of the ventral hyoid arch. " synonym: "basihyoid" synonym: "glossohyal” relationship: is_a TAO: 0001591 ! endochondral bone relationship: part_of TAO: 0001402 ! ventral hyoid arch relationship: develops_from TAO: 0001510 ! basihyal cartilage xref: ZFA: 0000316 endochondral bone ventral hyoid arch is_a basihyal cartilage part_of develops_from basihyal bone

Relationships among anatomical entities allow • Inference in an anatomical framework: A part_of B, B part_of C, then A part_of C • Data aggregation of anatomical entities by parent entities part_of hyoid arch is_a bone is_a dermal bone is_a frontal is_a sphenotic part_of is_a ventral hyoid arch endochondral bone is_a epihyal is_a ceratohyal part_of basihyal bone develops_from basihyal cartilage develops_from

The TAO in Phenoscape Linking data between evolutionary morphology and model species developmental genetics. species in a tree model org genotypes variable trait structure

Ontologies and Annotation Linking the content of interest to terms from ontologies PATO Trait ontology exhibits decreased Ostariophysi Gymnotiformes Apteronotidae Adontosternarchus nebulosus TAO Anatomy ontology size inheres in Entity-Quality phenotype statement ZFA Anatomy ontology PATO Trait ontology exhibits no tail genotype Zebrafish mutant caudal fin decreased size inheres in caudal fin Entity-Quality phenotype statement

Teleost ontology cloned from zebrafish ontology Zebrafish terms are is_a subtypes of teleost terms Teleost Anatomy Ontology Zebrafish Anatomy is_a

Requirements: addition of new anatomical terms • Ontology growth driven by annotation • Since cloning from Zebrafish Anatomy ontology in 2007, 686 (391 skeletal) new terms added; total = 2, 662 terms 1 mm middle nuchal plate anterior nuchal plate spinelet Catfish, Pimelodus maculatus Zebrafish, Danio rerio predorsal spine abdominal scutes False piranha, Catoprion mento

Annotation of evolutionary phenotypes using Phenex Term needed for annotation Entity TAO: suprapreopercle Quality PATO: decreased size Taxon TTO: Xenocharax spilurus

TAO development workflow

TAO development workflow

TAO development workflow OBO-Edit 2. 0

TAO development workflow

Challenge: managing ontology growth • New terms can be added to the ontology – Possess unique identifier – premaxilla ascending process TAO: 0000699 • is_a TAO: process • part_of TAO: premaxilla • Alternatively, terms can be “post-composed” at time of annotation by combining existing terms to create a new one: Entity TAO: process part_of TAO: premaxilla

Ontologies and Annotation Image annotation

Teleost Anatomy Ontology • Multi-species ontology that represents evolutionary variability • Logical challenges in representating variability across a clade in an ontology • Homology can be treated explicitly with a formalized relation between terms

Conclusions • Ontologies can be used to link evolutionary morphology and genetic data • Phenoscape is a prototype database for making this connection • Facilitates new discoveries (e. g. , candidate genes, patterns in morphological variability)