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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. 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.

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

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  1. 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

  2. Overview • Clientele • How we got started • Collaborative Ontology Building • Animal Trait Ontology

  3. Classification of Traits Chicken Chr1 GR BWt BWt BWt %AF BWt EWt_to AFE EN_to EN_to AFE MD_R MD_R GR %CARCASS BWt %SF BWt Body trait Infectious disease Reproduction female

  4. 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

  5. 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 ratio;meat color adjusted for body weight…

  6. 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

  7. Non-collaborative Ontology Building Download Ontology Upload Ontology Local Editing (single curator) (OBO-Edit) (Protégé)

  8. 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 Modular Ontology: Example

  9. General Pig 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

  10. The COB Editor Pig Package Cattle Package Chicken Package

  11. Reproduction Health Production Disease Resistance Reproduction Traits Pathogen Fertility Growth Daily Feed Intake White Blood Cell Count Salmonella Count in Liver Calving Ease Birth Weight Food Consumption Genetic Correlations ATO

  12. 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

  13. Acknowledgements • Sanger Institute • Sean Humphray • Carol Scott • Jane Rogers • UIUC • Stacey Meyers • Jonathan Beever • Dept. of Animal Sci., ISU • Max Rothschild • Eric Ryan Fritz • NCBI • Svetlana Dracheva • Donna Maglott • Wonhee Jang • USDA-MARC • Gary Rohrer Funding Provided by USDA-CSREES

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