1. 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

2. 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 In press. The Teleost Anatomy Ontology: Anatomical
representation for the genomics age. Systematic Biology.

3. Teleost Anatomy Ontology: TAO
Domain of knowledge: teleost anatomy

4. Teleost Anatomy Ontology: TAO
Domain of knowledge: teleost anatomy
“Preferred” terms for anatomical structures (entities) and their definitions 4

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 5

6. 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

7. 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

8. 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: ! endochondral bone
relationship: part_of TAO: ! ventral hyoid arch
relationship: develops_from TAO: ! basihyal cartilage
xref: ZFA:
basihyal
bone
endochondral
ventral hyoid arch
basihyal cartilage
is_a
part_of
develops_from

9. 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

10. 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

11. 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

12. 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

13. 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

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

15. TAO development workflow

16. TAO development workflow

17. TAO development workflow
OBO-Edit 2.0

18. TAO development workflow

19. Challenge: managing ontology growth
New terms can be added to the ontology
Possess unique identifier
premaxilla ascending process TAO:
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

20. Ontologies and Annotation
Image annotation

22. 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

23. 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)