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A controlled vocabulary for livestock phenotyping: the ATOL ontology

INRA Prod Anim 27(3) 195-208

P.-Y. LE BAIL¹, J. BUGEON¹, O. DAMERON², A. FATET³,⁴,⁵,⁶, W. GOLIK⁷, J.-F. HOCQUETTE⁸,⁹, C. HURTAUD¹⁰,¹¹ , I. HUE¹², C. JONDREVILLE¹³, L. JORET¹, M.-C. MEUNIER-SALAÜN¹⁰,¹¹, J. VERNET⁸,⁹, C. NEDELLEC⁷ , M. REICHSTADT⁸,⁹, P. CHEMINEAU³,⁴,⁵,⁶

1 INRA, UR1037 LPGP, F-35000 Rennes, France

2 Université de Rennes 1, IRISA, Dyliss team, F-35000 Rennes, France

3 INRA, UMR85 PRC, F-37380 Nouzilly, France

4 CNRS, UMR7247, F-37380 Nouzilly, France

5 Université François Rabelais de Tours, F-37000 Tours, France

6 IFCE, F-37380 Nouzilly, France

7 INRA, UR1077 MIG, F-78352 Jouy-en-Josas, France

8 INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle, France

9 Clermont Université, VetAgro Sup, UMR 1213 Herbivores, BP 10448, F-63000 Clermont-Ferrand, France

10 INRA, Agrocampus Ouest, UMR1348 PEGASE, F-35590 Saint-Gilles, France

11 Agrocampus Ouest, UMR1348 PEGASE, F-35000 Rennes, France

12 INRA, UMR1198 BDR, F-78352 Jouy-en-Josas, France

13 INRA, Université de Lorraine, USC340 AFPA, F-54500 Vandoeuvre-lès-Nancy, France

Abstract

Recent technological advances allow the production of large biological datasets that makes the description of phenotypes more accurate. To analyze this huge amount of information with computers and thus compare phenotypes, it is essential to define a standard language that unambiguously defines phenotypic traits so as to serve as a reference, worldwide, to any possible user (geneticist, physiologist, biochemist, modeler, producer...). The absence of such a language/reference for livestock species has led Inra, in collaboration with its international partners, to develop an ontology that is called ATOL (Animal Trait Ontology for Livestock). Its aims are to define the phenotypic characters of livestock species, and allocate them to different types: performance traits (feed efficiency, fertility), production traits (dairy, meat, eggs, fatty liver) and societal traits (welfare). This article summarizes the objectives of the project, the original approach used to build the ontology, but also its current status and performance as well as its limitation. This ontology is publicly available on the web and expected to be widely shared worldwide for the common use of unique terms to annotate publications, databases or mine literature and thus promote systemic as well as predictive biology.

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