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ATOL: The Multi-species Livestock Trait Ontology

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Metadata and Semantics Research (MTSR 2012)

Abstract

This paper presents the multi-species Animal Trait Ontology for Livestock (ATOL) and the methodology used for its design. ATOL has been designed as a reference source for indexing phenotype databases and scientific papers. It covers five major topics related to animal productions: growth and meat quality, animal nutrition, milk production, reproduction and welfare. It is composed of species-independent concepts subsuming species-specific ones so that cross-species and species-specific reasoning can be performed consistently. In order to ensure a large consensus, three complementary approaches have successively been applied to its design: reuse of existing ontologies, integration of production-specific livestock traits by a large team of domain experts and curators and terminology analysis of scientific papers. It resulted in a detailed taxonomy of 1,654 traits that is available at http://www.atol-ontology.com

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References

  1. Blake, J., Bult, C.: Beyond the data deluge: Data integration and bio-ontologies. Journal of Biomedical Informatics 39(3), 314–320 (2006)

    Article  Google Scholar 

  2. Hocquette, J.-F., Capel, C., David, V., Guéméné, D., Bidanel, J., Ponsart, C., Gastinel, P.-L., Le Bail, P.-Y., Monget, P., Mormède, P., Barbezant, M., Guillou, F., Peyraud, J.-L.: Objectives and applications of phenotyping network setup for livestock. Animal Science Journal 83, 517–528 (2012)

    Article  Google Scholar 

  3. Cimino, J.J., Zhu, X.: The practical impact of ontologies on biomedical informatics. Methods of Information in Medicine (2006)

    Google Scholar 

  4. Shah, N.H., Jonquet, C., Chiang, A.P., Butte, A.J., Chen, R., Musen, M.A.: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 10(suppl. 2), S1 (2009)

    Article  Google Scholar 

  5. Bard, J.B.L., Rhee, S.Y.: Ontologies in biology: design, applications and future challenges. Nature Reviews. Genetics 5(3), 213–222 (2004)

    Article  Google Scholar 

  6. Shimoyama, M., Nigam, R., Sanders McIntosh, L., Nagarajan, R., Rice, T., Rao, D.C., Dwinell, M.R.: Three ontologies to define phenotype measurement data. Frontiers in Genetics 3, 87 (2012)

    Article  Google Scholar 

  7. Smith, C.L., Goldsmith, C.-A.W., Eppig, J.T.: The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biology 6(1), 7 (2004)

    Article  Google Scholar 

  8. Hughes, L.M., Bao, J., Hu, Z.-L., Honavar, V., Reecy, J.M.: Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species. Journal of Animal Science 86(6), 1485–1491 (2008)

    Article  Google Scholar 

  9. Park, C., Bello, S., Smith, C., Hu, Z.-L., Munzenmaier, D., Shimoyama, M., Eppig, J., Reecy, J.: The vertebrate trait ontology: A controlled vocabulary to facilitate cross-species comparison of trait data. In: Proceedings of the 20th Conference on Plant and Animal Genomes, San Diego, CA (2012)

    Google Scholar 

  10. Uschold, M., King, M.: Towards a methodology for building ontologies. In: IJCAI 1995 Workshop on Basic Ontological Issues in Knowledge Sharing (1995)

    Google Scholar 

  11. Nédellec, C., Golik, W., Aubin, S., Bossy, R.: Building Large Lexicalized Ontologies from Text: A Use Case in Automatic Indexing of Biotechnology Patents. In: Cimiano, P., Pinto, H.S. (eds.) EKAW 2010. LNCS, vol. 6317, pp. 514–523. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  12. Mondary, T., Nazarenko, A., Zargayouna, H., Barreaux, S.: The quaero evaluation campaign on term extraction. In: Proceedings of the Eighth International Conference on Language Resources and Evaluation, LREC (2012)

    Google Scholar 

  13. Aussenac-Gilles, N., Després, S., Szulman, S.: The terminae method and platform for ontology engineering from texts. In: Bridging the Gap between Text and Knowledge - Selected Contributions to Ontology Learning and Population from Text, pp. 199–223 (2008)

    Google Scholar 

  14. Jacquemin, C.: A Symbolic and Surgical Acquisition of Terms Through Variation. In: Wermter, S., Scheler, G., Riloff, E. (eds.) IJCAI-WS 1995. LNCS, vol. 1040, pp. 425–438. Springer, Heidelberg (1996)

    Chapter  Google Scholar 

  15. Nédellec, C., Nazarenko, A., Bossy, R.: Information Extraction. In: Ontology Handbook, pp. 663–686. Springer (2008)

    Google Scholar 

  16. Miller, G.A., Beckwith, R., Fellbaum, C.D., Gross, D., Miller, K.: WordNet: An online lexical database. Int. J. Lexicograph. 3(4), 235–244 (1990)

    Article  Google Scholar 

  17. Bossy, R., Kotoujansky, A., Golik, W., Aubin, S., Nédellec, C.: Close integration of ML and NLP tools in BioAlvis for semantic search in bacteriology. In: Proc. of the Workshop on Semantic Web Applications and Tools for Life Sciences (2008)

    Google Scholar 

  18. AlvisIR for ANIMAL, http://bibliome.jouy.inra.fr/test/alvisir/animal/

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Golik, W. et al. (2012). ATOL: The Multi-species Livestock Trait Ontology. In: Dodero, J.M., Palomo-Duarte, M., Karampiperis, P. (eds) Metadata and Semantics Research. MTSR 2012. Communications in Computer and Information Science, vol 343. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35233-1_28

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  • DOI: https://doi.org/10.1007/978-3-642-35233-1_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-35232-4

  • Online ISBN: 978-3-642-35233-1

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