Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Developing Frameworks And Tools For Animal Trait Ontology (ATO)

Zhi-liang Hu¹ , Jie Bao^2,3 , Max F. Rothschild ¹ , Vasant Honavar^2,3 , James M. Reecy ¹

¹  Department of Animal Science and Center for Integrated Animal Genomics, 2255 Kildee Hall, Iowa State University, Ames, IA 50011

²  Department of Computer Science, Iowa State University, Ames, IA 50011

³  Center for Computational Intelligence, Learning, and Discovery, 226 Atanasoff Hall, Iowa State University, Ames, IA 50011

There is an urgent need for precise definition of animal trait terms (phenotypes) to capture the biologically relevant distinctions at the desired level of detail in an unambiguous fashion. Ontologies that identify and define the entities and relationships in specific domains of interest offer a powerful approach for annotating biological data in a form that allows users and software tools to retrieve, inter-relate, and extract biological knowledge. Our previous work on PigQTLdb introduced simple ontologies in the form of controlled vocabularies to describe pig phenotypes/traits. We now turned our attention to the development of software tools to facilitate the creation, editing, curation, and management of animal trait ontologies. We have developed an animal trait ontology editor (ATO editor) that overcomes the most of these problems. We have also developed database structures to manage trait ontology for cattle, pigs, chickens, sheep and other livestock species. To date, we have entered over 300 pig traits into the ontology database. In order for such ontologies to be broadly useful to the livestock and animal genomics communities, they need to capture the knowledge and expertise of multiple experts and research groups. Hence, we propose the creation of consortia representing the relevant livestock genome communities to develop, maintain, and update trait ontologies. ATO and associated software tools for collaborative creation, editing, curation, and management of ontologies provide the infrastructure necessary for engaging the animal genomics and livestock communities in the process of creating comprehensive genomic resources for annotating, integrating, and analyzing phenotype and genomic data.