L. Hughes, J. Bao, Z.-L. Hu, V. Honavar, J.M. Reecy

Iowa State University

Animal Trait Ontology

A Project for the Creation of a Unified Trait Vocabulary for Farm

Animals

Overview

• Clientele• How we got started• Collaborative Ontology

Building• Animal Trait Ontology

Classification of TraitsClassification of Traits

BW

tB

Wt

BW

tB

Wt

%A

FG

R%

CA

RC

AS

S

BW

t

GR

BW

t

%S

F

Body trait

MD

_RM

D_R

Infectious disease

EN

_to

AFE

EW

t_to

EN

_to

AFE

Reproduction female

Chicken Chr1

AIMS

• Form a collaborative group to develop an Animal Trait Ontology (ATO) – Include trait information for the pig, chicken, cow,

and other farm animals• Form a collaborative effort between the ATO

and other species ontology’s • Create a database that will allow the linkage of

the trait information for each species stored in the ontology to its qtl/gene expression/proteomic information

Classification ofClassification of TraitsTraits

- Define a 3 level Ontology based on the different publications : Body traits Behaviour Immune response Infectious disease Metabolic disease Reproduction

- Interactions between traits or traits belonging to different group : Thigh meat / bone ratio;meat color adjusted for body weight…

- Mammalian Phenotype Ontology (MGI website) not suitable for production traits.

- Define a 3 level Ontology based on the different publications : Body traits Carcass traits

Fat Growth traits Meat quality Metabolic traits Muscular system Nervous system Organs Plumage Skeletal system

- Define a 3 level Ontology based on the different publications : Body traits

Fat % Abdominal fat weight Abdominal fat weight Abdominal fat weight / BW Abdominal fat width Fat distribution Skin fat weight Skin fatness

• Each package can be independently developed

• Different curators can concurrently edit the ontology on different packages

• Ontology can be only partially loaded• Module access privileges can be controlled

by the package hierarchy• Unwanted interactions are minimized by

limiting term and axiom visibility

Collaborative Ontology Building (COB) Editor

Non-collaborative Ontology Building

DownloadOntology Local Editing

UploadOntology

(single curator)

(Protégé) (OBO-Edit)

Modular Ontology: Example

Swine

Cattle Chicken

Horse

Each group works on an ontology module for a particular species (according to the group’s best expertise)

Collaborative building of an animal trait ontology that involves multiple research groups across the world

• A nested package is a part of another package

• Could be used to represent the organizational structure of an ontology– Arrange knowledge– Enforce hierarchical

management of knowledge

General

Pig Health

Pig

Animal trait ontology

Package Nesting

The COB EditorPig Package

Cattle PackageChicken Package

WhiteBlood Cell

Count

SalmonellaCount in

LiverFood

ConsumptionCalving

Ease

FertilityReproduction

TraitsPathogen GrowthDaily Feed Intake

DiseaseResistance

ATO

Reproduction ProductionHealth

BirthWeight

Genetic Correlations

Contributions• A unified vocabulary for farm animals

phenotypic traits

• COB Editor provides the necessary tool to collaboratively build well-structured, large-scale, biomedical ontologies

• Higher order ontology terms that link species

Acknowledgements

UIUC • Stacey Meyers • Jonathan Beever

Sanger Institute • Sean Humphray• Carol Scott• Jane Rogers

USDA-MARC • Gary Rohrer

Dept. of Animal Sci., ISU• Max Rothschild• Eric Ryan Fritz

NCBI• Svetlana Dracheva• Donna Maglott• Wonhee Jang

Funding Provided by USDA-CSREES