l. hughes, j. bao, z.-l. hu, v. honavar, j.m. reecy iowa state university animal trait ontology a...
TRANSCRIPT
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