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

t

BW

t

BW

t

BW

t%

AF

GR

%C

AR

CA

SS

BW

t

GR

BW

t

%S

F

Body trait

MD

_R

MD

_R

Infectious disease

EN

_to

AF

E

EW

t_to

EN

_to

AF

E

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 Editor

Pig Package

Cattle Package

Chicken Package

WhiteBlood Cell

Count

SalmonellaCount in

Liver

FoodConsumption

CalvingEase

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