REProduction Ontology (REPO)

Introduction

The need for biological ontologies has risen in recent years in large part due to the rapid increase of the use of databases and other bioinformatics tools. Successful ontologies in biology have emerged in the past few years, such as Gene Ontology, Rice Ontology, Plant Phenotype and Trait Ontology. In animal sciences there is a need for an Animal Trait Ontology (ATO). 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. This helps to correctly link phenotypic data to structural and functional genome information in various databases, and allows meaningful comparisons within and between species.

Within the framework of two EU funded projects, ongoing work is focusing on the development of an ATO in the fields of host-pathogen interactions (EADGENE) and reproduction (SABRE). The objective is to develop ATO sub-domains by including relevant trait information for selected animals species and to create a database that allows the linkage of the trait with other information (QTLs, SNPs, mRNA, protein, etc.) within and across species including mouse, rat, and human. In this context, there is a collaboration between the U.S. (James Reecy, NRSP-8 Animal Trait Ontology Project) and Europe (Hein van der Steen, ATO coordinator, EADGENE and SABRE) with the objective of developing a unified ATO.

The Need for a REProduction Ontology

Reproduction is an important characteristic of farm animal species. Especially in dairy cattle fertility and calving traits are of significant economic importance. These traits are regulated by an unknown number of genes, and are strongly influenced by a variety of environmental factors. Gene profiling studies in this area are of relative recent date, but since the technical possibilities to perform such studies are growing rapidly, a strong increase in the availability of molecular information can be expected over the next few years. Consequently, a vast amount of information about reproduction in dairy cattle will be acquired, stored and displayed in various formats and media, both electronically and otherwise. In order to make a real contribution to a better understanding of reproduction in dairy cattle, it is necessary that as much as possible pertinent information is brought together in a broadly accessible ontology. This ontology for farm animal reproduction will be valuable for animal production scientists, veterinary scientists and bio-medical scientists, as well as for industry. Within the EU project SABRE (work packages 3 and 6) we have developed the first outlines of such an ontology for reproduction in farm animals (REPO).

REPO development

The current version of REPO includes the major terms for the domain female fertility in cattle, together with their synonyms and, in most cases, text definitions. The terms have been collected from expert knowledge, from literature, from thesauruses and from existing ontologies. The top level terms of REPO include; reproductive behaviour; reproductive failure; and reproductive performance. This REPO has been developed in such a way that it can easily be integrated with ATO (http://www.animalgenome.org/bioinfo/projects/ATO/).

The ontology is constructed using the open source, stand alone application Protégé (http://protege.stanford.edu/). The language used for building the ontology was the Web Ontology Language also called OWL (http://www.w3.org/TR/owl-features/). The OWL is a semantic markup language for publishing and sharing ontologies on the World Wide Web. OWL is recommended by W3C as an international standard for ontologies on the web.

A screen shot from Protégé of REPO

Download the Reproduction Ontology

The Reproduction Ontology is available for download in Protege-OWL format. Please click here to download the zipped file.

Communication

We realize the importance of community input for the development of REPO in order to create a vocabulary for research and representation. We invite reproduction experts to contribute to the elaboration of REPO, suggesting new concepts, new relations between classes or anything else, and contacting us by e-mail. Moreover, if you have interesting ideas, suggestions and/or criticisms about ontology for farm animal reproduction, please let us know.

Contacts:
Ina Hulsegge: Ina.Hulsegge@wur.nl
Henri Woelders: henri.woelders@wur.nl