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

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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
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Overview

• Clientele
• How we got started
• Collaborative Ontology Building
• Animal Trait Ontology

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Classification of Traits
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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 ontologys
• 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

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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 ?
Behaviour ? Immune response ? Infectious
disease ? Metabolic disease ? Reproduction
- 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
- Interactions between traits or traits belonging
to different group Thigh meat / bone ratiomeat
color adjusted for body weight
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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

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Non-collaborative Ontology Building
Download Ontology
Upload Ontology
Local Editing
(single curator)
(OBO-Edit)
(Protégé)
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Modular Ontology Example
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Package Nesting

• 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

Animal trait ontology
Pig Health
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The COB Editor
Pig Package
Cattle Package
Chicken Package
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ATO
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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

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Acknowledgements

• Sanger Institute
• Sean Humphray
• Carol Scott
• Jane Rogers

• UIUC
• Stacey Meyers
• Jonathan Beever

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

• USDA-MARC
• Gary Rohrer

• NCBI
• Svetlana Dracheva
• Donna Maglott
• Wonhee Jang

Funding Provided by USDA-CSREES