Animal Trait Ontology Project|
Developing Frameworks and Tools for the Livestock Community
The need for biological ontologies has risen in recent years in large part due to the rapid development of large biological databases. Successful ontologies in biology have emerged in the past few years, such as Gene Ontology, Rice Ontology, Plant Phenotype and Trait Ontology.
Precise definition of animal trait terms (phenotypes) will help to capture the biologically relevant distinctions at the desired level of detail in an unambiguous fashion. It helps to correctly link the data to genome information in a database, and to allow meaningful comparisons. Previous work by Hu et al (2005) on the PigQTLdb introduced simple ontologies in the form of controlled vocabularies to describe pig phenotypes/ traits and linked them to QTL information. This was further developed to serve similar purpose for other livestock species as well (e.g. cattle, chicken, sheep, rainbow trout; see Hu et al 2007, 2010 ).
We have begun working with Mouse Genome Informatics, the Rat Genome Database, European Animal Disease Genomics Network of Excellence (EADGENE) and the French National Institute for Agricultural Research (INRA) to incorporate the Mammalian Phenotype (MP) ontology and the ATO to develop a Vertebrate Trait Ontology (VT). This project is aimed at enhancing the ability to standardize phenotype nomenclature across species. This will undoubtedly help the pig genome community by facilitating the transfer of genomics information from some well studied species.
The current ATO data is edited from that in the Animal QTLdb. The traits (ontology) can be browsed for viewing with the popular ontology browser AmiGO. (Click here to start).
Existing ontology editing tools, such as the DAG-Edit (Day-Richter, 2004), did not seamlessly meet our needs, especially when there are demands for collaborativeness and scalability. We have created the Collaborative Ontology Builder (COB, Editor) to overcome these difficulties and provide a tool for the animal genetics/genomics community at large. Here is an example of the software window. You can download the tool and try it out. If you are interested to involve in the development of animal trait ontology, please fee freel to visit our SourceForge site .Features Highlights
Collaborativeness Ontology building is a collaborative process. In order for an ontology to be broadly useful to a certain community, it needs to capture the knowledge based on the collective expertise of multiple experts and research groups. Typically, a large ontology is built and curated by a community.
Scalability Stronger tools are needed to handle large-scale ontology for storage, editing, browsing, visualizing, reasoning and reusing. Those tools should enable processing of the ontology with limited time and space resources. Such characteristics call for mechanism and tools to support both scaleable and collaborative ontology building.
The ATO project is a community consortium, which needs inputs from all who wish to contribute and collaborate. You are welcome to join the consortium. See "To Participate" for more details.(Last updated: September 9, 2012)