Download Animal trait ontology

Animal Trait Ontology
A Project for the Creation of a
Unified Trait Vocabulary for Farm
Animals
L. Hughes, J. Bao, Z.-L. Hu, V. Honavar, J.M. Reecy
Iowa State University
Overview
• Clientele
• How we got started
• Collaborative Ontology
Building
• Animal Trait Ontology
Classification of Traits
Body
trait
AFE
EWt_to
EN_to
AFE
MD_R
GR
%SF
BWt
BWt
%CARCASS
MD_R
EN_to
BWt
BWt
%AF
BWt
BWt
GR
Chicken Chr1
Infectious
disease
Reproduction
female
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 of
Traits
- 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
 % Abdominal fat weight
 Behaviour
 Abdominal fat weight
 Growth traits
 Immune response  Meat quality
 Abdominal fat weight / BW
 Abdominal fat width
 Infectious disease  Metabolic traits
 Fat distribution
 Muscular system
 Skin fat weight
 Metabolic disease
 Nervous system
 Skin fatness
 Reproduction
 Organs
 Plumage
 Skeletal system
- Interactions between traits or traits belonging to different group : Thigh
meat / bone ratio;meat color adjusted for body weight…
Collaborative Ontology Building
(COB) Editor
• 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
Non-collaborative Ontology
Building
Download
Ontology
Local Editing
Upload
Ontology
(single curator)
(Protégé)
(OBO-Edit)
Modular Ontology: Example
Collaborative building of an animal
trait ontology that involves multiple
research groups across the world
Swine
Horse
Each group works on an ontology
module for a particular species
(according to the group’s best expertise)
Cattle
Chicken
Package Nesting
Animal trait ontology
General
Pig
Pig Health
• 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
The COB Editor
Pig Package
Cattle Package
Chicken Package
ATO
Reproduction
Health
Disease
Resistance
White
Blood Cell
Count
Pathogen
Salmonella
Count in
Liver
Fertility
Calving
Ease
Production
Reproduction
Traits
Birth
Weight
Genetic Correlations
Growth
Daily
Feed
Intake
Food
Consumption
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
Sanger Institute
• Sean Humphray
• Carol Scott
• Jane Rogers
UIUC
Dept. of Animal Sci., ISU
• Stacey Meyers
• Jonathan Beever
• Max Rothschild
• Eric Ryan Fritz
NCBI
USDA-MARC
• Svetlana Dracheva
• Donna Maglott
• Wonhee Jang
• Gary Rohrer
Funding Provided by USDA-CSREES