e-infrastructure Roadmap for Open Science in Agriculture

A bibliometric study

The e-ROSA project seeks to build a shared vision of a future sustainable e-infrastructure for research and education in agriculture in order to promote Open Science in this field and as such contribute to addressing related societal challenges. In order to achieve this goal, e-ROSA’s first objective is to bring together the relevant scientific communities and stakeholders and engage them in the process of coelaboration of an ambitious, practical roadmap that provides the basis for the design and implementation of such an e-infrastructure in the years to come.

This website highlights the results of a bibliometric analysis conducted at a global scale in order to identify key scientists and associated research performing organisations (e.g. public research institutes, universities, Research & Development departments of private companies) that work in the field of agricultural data sources and services. If you have any comment or feedback on the bibliometric study, please use the online form.

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Comparison of methods for the implementation of genome-assisted evaluation of Spanish dairy cattle


The aim of this study was to evaluate methods for genomic evaluation of the Spanish Holstein population as an initial step toward the implementation of routine genomic evaluations. This study provides a description of the population structure of progeny tested bulls in Spain at the genomic level and compares different genomic evaluation methods with regard to accuracy and bias. Two Bayesian linear regression models, Bayes-A and Bayesian-LASSO (B-LASSO), as well as a machine learning algorithm, Random-Boosting (R-Boost), and BLUP using a realized genornic relationship matrix (G-BUR), were compared. Five traits that are currently under selection in the Spanish Holstein population were used: milk yield, fat yield, protein yield, fat percentage, and udder depth. In total, genotypes from 1859 progeny tested bulls were used. The training sets were composed of bulls born before 2005; including 1601 bulls for production and 1574 bulls for type, whereas the testing sets contained 258 and 235 bulls born in 2005 or later for production and type, respectively. Deregressed proofs (DRY) from January 2009 Interbull (Uppsala, Sweden) evaluation were used as the dependent variables for bulls in the training sets, whereas DRP from the December 2011 DRPs Interbull evaluation were used to compare genomic predictions with progeny test results for bulls in the testing set. Genomic predictions were more accurate than traditional pedigree indices for predicting future progeny test results of young bulls. The gain in accuracy, due to inclusion of genomic data varied by trait and ranged from 0.04 to 0.42 Pearson correlation units. Results averaged across traits showed that B-LASSO had the highest accuracy with an advantage of 0.01, 0.03 and 0.03 points in Pearson correlation compared with R-Boost, Bayes-A, and G-BLUP, respectively. The B-LASSO predictions also showed the least bias (0.02, 0.03 and 0.10 SD units less than Bayes-A, R-Boost and G-BLUP, respectively) as measured by mean difference between genomic predictions and progeny test results. The R-Boosting algorithm provided genomic predictions with regression coefficients closer to unity, which is an alternative measure of bias, for 4 out of 5 traits and also resulted in mean squared errors estimates that were 2%, 10%, and 12% smaller than B-LASSO, Bayes-A, and G-BLUP, respectively. The observed prediction accuracy obtained with these methods was within the range of values expected for a population of similar size, suggesting that the prediction method and reference population described herein are appropriate for implementation of routine genome-assisted evaluations in Spanish dairy cattle. R-Boost is a competitive marker regression methodology in terms of predictive ability that can accommodate large data sets.

  • ES
  • Univ_Politecn_Madrid_UPM (ES)
  • INIA_Natl_Inst_Agr_&_Food_Res_&_Technol (ES)
Data keywords
  • machine learning
Agriculture keywords
  • cattle
Data topic
  • big data
  • modeling
Document type

Inappropriate format for Document type, expected simple value but got array, please use list format

Institutions 10 co-publis
  • Univ_Politecn_Madrid_UPM (ES)
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e-ROSA - e-infrastructure Roadmap for Open Science in Agriculture has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730988.
Disclaimer: The sole responsibility of the material published in this website lies with the authors. The European Union is not responsible for any use that may be made of the information contained therein.