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 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 4

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 5

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 6

An example from the Teleost Anatomy Ontology basihyal bone endochondral bone ventral hyoid arch basihyal cartilage is_a part_of develops_from 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 basihyal bone endochondral ventral hyoid arch basihyal cartilage is_a part_of develops_from

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 develops_from part_of endochondral bone ventral hyoid arch basihyal cartilage is_a epihyal ceratohyal bone dermal bone sphenotic frontal basihyal hyoid arch

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

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

Zebrafish terms are is_a subtypes of teleost terms Teleost ontology cloned from zebrafish ontology Zebrafish terms are is_a subtypes of teleost terms Zebrafish Anatomy Teleost Anatomy Ontology is_a 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 Zebrafish, Danio rerio middle nuchal plate predorsal spine spinelet anterior nuchal plate abdominal scutes Catfish, Pimelodus maculatus False piranha, Catoprion mento

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