With the advent of sequencing projects in model organisms, humans, and domesticated livestock species, the need for storage, retrieval, and analysis of genomics information for these animals has become important. The Animal Trait Ontology (ATO) is an ontology that has been created to store the relationships between farm animal traits for several domesticated farm animals. The Collaborative Ontology Building (COB) editor was used to create and edit the ATO. An online ontology browser has been developed to search and browse the ontology and to view the relationships between the terms. Some of the traits in the ontology are linked to associated quantitative trait loci (QTL) information for each species through a tool called the Comparative Animal QTL (CAQ) tool which allows users to compare QTL experiments in livestock species. The tool allows QTL experiments to be compared based on (1) one trait given one species, and (2) two traits given one species. The effectiveness of the tool is recorded in the form of a data and statistical analysis which demonstrates its use in examining pleiotropic effects for traits in the pig. In addition, the Human and Animal Trait Ontology is discussed and it will form an agglomeration of several different species ontologies, including the ATO, that will form a consensus for describing phenotypes and traits across different disease models.