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ATOL: The Multi-species Livestock Trait Ontology [chapter]

Wiktoria Golik, Olivier Dameron, Jérôme Bugeon, Alice Fatet, Isabelle Hue, Catherine Hurtaud, Matthieu Reichstadt, Marie-Christine Salaün, Jean Vernet, Léa Joret, Frédéric Papazian, Claire Nédellec (+1 others)
2012 Communications in Computer and Information Science  
This paper presents the multi-species Animal Trait Ontology for Livestock (ATOL) and the methodology used for its design.  ...  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  ...  In this paper, we describe the ATOL multi-species livestock trait ontology, the motivation and its design method.  ... 
doi:10.1007/978-3-642-35233-1_28 fatcat:vloi43ivjff47aslnd2udwtwz4

Multi-site evaluation of the rearing performances of 5 wild populations of European sea bass (Dicentrarchus labrax)

Marc Vandeputte, Romain Garouste, Mathilde Dupont-Nivet, Pierrick Haffray, Alain Vergnet, Hervé Chavanne, Stanislas Laureau, Tetsuzan Benny Ron, Glen Pagelson, Carlos Mazorra, Rémi Ricoux, Pedro Marques (+2 others)
2014 Aquaculture  
Acknowledgements This work is part the COMPETUS project, funded by Ardag Red Sea Mariculture (Eilat,  ...  Trait Tagging body weight ( 2±0.4% a * trait identifier according to Animal Trait Ontology for Livestock http://www.atol-ontology.com/index.php/en/les-ontologies-en/visualisation-en (1) studied as ln  ...  The fish traits measurements indexed according to the ATOL fish trait ontology (http://www.atol-ontology.com/index.php/en/les-ontologies-en/visualisation-en, Golik et al., 2012) .  ... 
doi:10.1016/j.aquaculture.2014.01.005 fatcat:55gpwltdzvci7dfjjszxc4ygke

First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements

Marc Vandeputte, Jérôme Bugeon, Anastasia Bestin, Alexandre Desgranges, Jean-Michel Allamellou, Anne-Sophie Tyran, François Allal, Mathilde Dupont-Nivet, Pierrick Haffray
2019 Frontiers in Genetics  
Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the  ...  At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting.  ...  The traits measured and the rearing environments were indexed according to the ATOL ontology (Animal Trait Ontology for Livestock) and EOL (Environment Ontology for Livestock) available on ATOL (http:/  ... 
doi:10.3389/fgene.2019.01225 pmid:31921286 pmcid:PMC6933014 fatcat:hosbzklogjapdd2p4p2cnrxpge

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
Database URL: https://www.agbiodata.org CMO http://obofoundry.org/ontology/cmo.html Crop Ontology a collection of vocabularies that describe breeders' traits for agriculturally important plants: banana  ...  As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

AgroPortal: A vocabulary and ontology repository for agronomy

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018 Computers and Electronics in Agriculture  
The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata  ...  By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain.  ...  We also thank the National Center for Biomedical Ontologies for their help and time spent with us in deploying the AgroPortal.  ... 
doi:10.1016/j.compag.2017.10.012 fatcat:tsvou7l42bg5hn6cw43ogtj2je

Classification and analysis of a large collection of in vivo bioassay descriptions

Magdalena Zwierzyna, John P. Overington, Nir London
2017 PLoS Computational Biology  
Yet, despite the importance of such experiments for translational medicine, there have been relatively few efforts to comprehensively and consistently analyze the data produced by in vivo bioassays.  ...  strains, experimental treatments, and phenotypic readouts used in the experiments.  ...  We also thank Aroon Hingorani at the Institute of Cardiovascular Science, UCL, London for discussions around the interface with clinical science.  ... 
doi:10.1371/journal.pcbi.1005641 pmid:28678787 pmcid:PMC5517062 fatcat:oqirndgpv5cw3k77y2cbesyx7i

Standard genetic nomenclature [chapter]

Z. L. Hu, J. M. Reecy, F. McCarthy, C. A. Park
The genetics of cattle  
Therefore, this chapter will only concentrate on discussions about the issues involved in the standardization of gene and trait terminologies. Disciplines  ...  Genetic terms describe processes, genes and traits with which genetic phenomena are examined and described.  ...  Acknowledgements The authors wish to thank Dr Frank Nicholas from the University of Sydney for useful discussions, inputs and kind review of the draft.  ... 
doi:10.1079/9781780642215.0598 fatcat:b5h3hgsrhnfgtiijzfkjqjskje

Agriculture and Digital Technology: Getting the most out of digital technology to contribute to the transition to sustainable agriculture and food systems

Véronique Bellon Maurel, Frédérick Garcia, Ludovic Brossard, Nathalie Mitton, Alexandre Termier
2022
Multi-objective decision-making in agroecology Co-designing innovative agricultural equipment and agroecosystems 4.3 Improving integration within the agricultural regional or economic ecosystem Agricultural  ...  3.3 Multi-scale learning and knowledge extraction Massive data in agriculture Data pre-processing Supervised approaches Unsupervised approaches Reinforcement learning Data warehouses and OLAP analysis  ...  The network currently consists of three web ontologies (Salaun et al., 2018) : Animal Trait Ontology for Livestock (ATOL, on phenotypic traits in livestock), Environment Ontology for Livestock (EOL, on  ... 
doi:10.17180/wmkb-ty56-en fatcat:o4l6kbeo5feqhp7o3kedhbohxq

Proceedings of the XIIIth International Symposium on Ruminant Physiology (ISRP 2019)

2019 Advances in Animal Biosciences  
The development of the cattle ontology of traits (ATOL and EOL; www.atol-ontology.com) through SmartCow will help to unify research methodologies and link trait definition with standardized methods.  ...  in livestock production.  ...  Their use in ruminant feeding could alleviate this problem and contribute to a more sustainable livestock production.  ... 
doi:10.1017/s2040470019000037 fatcat:hpfsjzye5nhznghzjci37jvwie

Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Carole Blay, Pierrick Haffray, Jonathan D'Ambrosio, Enora Prado, Nicolas Dechamp, Virginie Nazabal, Jérôme Bugeon, Florian Enez, David Causeur, Christophe Eklouh-Molinier, Vincent Petit, Florence Phocas (+2 others)
2021
found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait.  ...  This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species.  ...  All measured traits were defined according to the ATOL (Animal Trait Ontology for Livestock) database, available online (https://www.atol-ontology.com/en/).  ... 
doi:10.1186/s12864-021-08062-7 pmid:34732127 fatcat:zjfhtivtkndmngt6mitvw3am3y

Eos, Transactions, American Geophysical Union Volume 87, Number 16, 18 April 2006

2006 EOS  
climate over the time or in the geographic range of the species in question.  ...  The symposium's primary objective is to present a synthesis of the effects of seasonal to multi-decadal variability on the structure and function of the North Pacific.  ... 
doi:10.1029/eost2006eo16 fatcat:ih27okgxevd3hfa4w7nn6qyoju

Like a Virgil: Georgic Ontologies of Agrarian Work in Canadian Literature [article]

Jennifer Baker, University, My, University, My
2019
and realities of agricultural production in Canada precisely because it is a literary genre that focuses on the labour of farming and because it constitutes a complex and multi-generic discourse which  ...  Critics of Canadian literature have tended to subsume the georgic under the category of pastoral, but I argue that the georgic is a separate and more useful category for understanding the complex myths  ...  atoll?"  ... 
doi:10.20381/ruor-23427 fatcat:gezjq2fe6nay3iwtmyuut5u4wq

Whole Issue//Número completo

Imelda Martin Junquera
2016 Ecozon@  
Seventy percent of global agricultural land is dedicated to livestock production, and livestock account for 18% of total greenhouse gas emissions because of enteric fermentation-the internal microbes in  ...  (Traité 211) The solitary life of the statue is "une vie purement animale." What is missing that could radically change its mind is language.  ...  During the second half of the nineteenth century, the lowlands of the Duchy of Brunswick in Northern Germany emerged as a prime sugar beet growing area due to the fertile topsoil in the broad Oker river  ... 
doi:10.37536/ecozona.2016.7.1.972 fatcat:kq256iepzjakngbgosrnhwcgiq

Cambodian Journal of Natural History Cambodian Journal of Natural History

Dr, Knud Heller, Nykøbing Zoo, Sovanmoly Hul, Dr, Andy Maxwell, Dr, Jörg Menzel, Dr, Campbell Webb
2015 unpublished
We thank the many staff and volunteers who, over the years, have collected survey data with us on the Cambodia Reef Conservation Project (CRCP) at CCC.  ...  We also thank the UK Government's Darwin Initiative and the Blue Moon Fund for providing fi nancial assistance to our project.  ...  The site is part of Rennell Island, the largest raised coral atoll in the world.  ... 
fatcat:d6335jyq2jecrosnvbvvt7mn3i

Kanak coastal communities and fisheries meeting new governance challenges and marine issues in New Caledonia [chapter]

Samuel Cornier, Isabelle Leblic
Fisheries in the Pacific  
The 14 Pacific SIDS are the Cook Islands, the Federated States of Micronesia (FSM), Fiji, Kiribati, Nauru, Niue, Palau, Papua New Guinea (PNG), the Republic of the Marshall Islands (RMI), Samoa, the Solomon  ...  In addition, the Pacific is one of the most remote and far flung regions in the world (AusAID 2008: 1).  ...  of Ngulu, Nukuoro and Kapingamarangi Atolls.  ... 
doi:10.4000/books.pacific.434 fatcat:5nbhv67cofadxjwq3rct3ko36m
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