1. 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

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

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

10. 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

11. Classification of Traits Traits - 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

12. 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

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

14. Modular Ontology: Example Swine CattleChicken 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

15. 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

16. The COB Editor Pig Package Cattle Package Chicken Package

17. White Blood Cell Count Salmonella Count in Liver Food Consumption Calving Ease Fertility Reproduction Traits PathogenGrowth Daily Feed Intake Disease Resistance ATO Reproduction ProductionHealth Birth Weight Genetic Correlations

18. 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

19. 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