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Genebanks and genomics: how to interconnect data from both communities?

Published online by Cambridge University Press:  27 May 2014

Richard Finkers ,
Pierre-Yves Chibon ,
Rob van Treuren ,
Richard Visser  and
Theo van Hintum
Richard Finkers*
Affiliation:
Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
Pierre-Yves Chibon
Affiliation:
Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
Rob van Treuren
Affiliation:
Centre for Genetic Resources, Wageningen University and Research Centre, Wageningen, The Netherlands
Richard Visser
Affiliation:
Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
Theo van Hintum
Affiliation:
Centre for Genetic Resources, Wageningen University and Research Centre, Wageningen, The Netherlands
*
*Corresponding author. E-mail: richard.finkers@wur.nl
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Abstract

Genebanks are important suppliers of genetic resources to the genomics research community, and access to the resulting information will allow traditional genebank users to better select genetic material for their breeding and scientific programmes. We discuss herein a possible solution to interconnect these data automatically based on semantic web technology.

Keywords

data integrationgenebank communitygenomics communitysemantic web
Type
Short Communication
Information
Plant Genetic Resources , Volume 13 , Issue 1 , April 2015 , pp. 90 - 93
Copyright
Copyright © NIAB 2014 

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References

Anguita, A, García-Remesal, M, de la Iglesia, D and Maojo, V (2013) NCBI2RDF: Enabling full RDF-based access to NCBI databases. Biomed Research International 2013: 983805.CrossRefGoogle ScholarPubMed
EU-SOL BreeDB (2013) Available at https://www.eu-sol.wur.nl (accessed November 8 2013).Google Scholar
Finkers, R, Smit, S, Peters, S, Schijlen, E, van Heusden, AW and Zhang, G (2012) 150 Tomato genome (re-) sequencing project. In: 9th Solanaceae Conference, Neuchâtel, Switzerland.Google Scholar
GCP (2013) Crop ontology curation tool, a service of the GCP integrated breeding platform. Available at http://www.cropontology.org (accessed November 8 2013).Google Scholar
Lam, HM, Xu, X, Liu, X, Chen, W, Yang, G, Wong, FL, Li, MW, He, W, Qin, N, Wang, B, Li, J, Jian, M, Wang, J, Shao, G, Wang, J, Sun, SSM and Zhang, G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42: 1053–1059.CrossRefGoogle ScholarPubMed
Matteis, L, Chibon, P-Y, Espinosa, H, Skofic, M, Finkers, R, Bruskiewich, R, Hyman, G and Arnaud, E (2013) Crop ontology: vocabulary for crop-related concepts. In: Proceedings of the First International Workshop on Semantics for Biodiversity, vol. 979, 27 May 2013, Montpellier, France.Google Scholar
McCouch, SR, McNally, KL, Wang, W and Sackville Hamilton, R (2012) Genomics of gene banks: a case study in rice. American Journal of Botany 99: 407–423.CrossRefGoogle Scholar
Pohorec, S, Zorman, M and Kokol, P (2013) Analysis of approaches to structured data on the web. Computer Standards & Interfaces 36: 256–262.CrossRefGoogle Scholar
Redaschi, N and Uniprot Consortium, (2009) UniProt in RDF: tackling data integration and distributed annotation with the semantic web. Nature Precedings 272: 21784–21792.Google Scholar
SemGem (2013) Semantic genebank integration, prototype software for the integration of data of a breeding database with those of a genebank. Available at https://github.com/PBR/SemGem (accessed January 2014).Google Scholar
van Treuren, R and van Hintum, TJL (2014) Next-generation genebanking: plant genetic resources management and utilization in the sequencing era. Plant Genetic Resources Characterization and Utilization 12: 298–307.CrossRefGoogle Scholar
W3C(2008) SPARQL query language for RDF. Available at http://www.w3.org/TR/rdf-sparql-query (accessed January 7 2014).Google Scholar
W3C(2013) Semantic web. Available at http://www.w3.org/standards/semanticweb (accessed 30 October 2013).Google Scholar
Xu, X, Liu, X, Ge, S, Jensen, JD, Hu, F, Li, X, Dong, Y, Gutenkunst, RN, Fang, L, Huang, L, Li, J, He, W, Zhang, G, Zheng, X, Zhang, F, Li, Y, Yu, C, Kristiansen, K, Zhang, X, Wang, J, Wright, M, McCouch, S, Nielsen, R, Wang, J and Wang, W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30: 105–111.CrossRefGoogle Scholar