Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy
Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Public Library of Science
2018
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| Acceso en línea: | https://hdl.handle.net/10568/99412 |
| _version_ | 1855522824758755328 |
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| author | Venkatesan, A. Tagny Ngompe, G. El Hassouni, N. Chentli, I. Guignon, Valentin Jonquet, C. Ruíz, M. Larmande, Pierre |
| author_browse | Chentli, I. El Hassouni, N. Guignon, Valentin Jonquet, C. Larmande, Pierre Ruíz, M. Tagny Ngompe, G. Venkatesan, A. |
| author_facet | Venkatesan, A. Tagny Ngompe, G. El Hassouni, N. Chentli, I. Guignon, Valentin Jonquet, C. Ruíz, M. Larmande, Pierre |
| author_sort | Venkatesan, A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to effectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies. We have developed the Agronomic Linked Data (AgroLD– www.agrold.org), a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, arabidopsis. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources–such as Gramene.org and TropGeneDB–with 10 ontologies–such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD’s objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach. |
| format | Journal Article |
| id | CGSpace99412 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace994122025-11-12T05:41:06Z Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy Venkatesan, A. Tagny Ngompe, G. El Hassouni, N. Chentli, I. Guignon, Valentin Jonquet, C. Ruíz, M. Larmande, Pierre ontology agronomy genes information retrieval knowledge organization system computer applications cereal crops Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to effectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies. We have developed the Agronomic Linked Data (AgroLD– www.agrold.org), a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, arabidopsis. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources–such as Gramene.org and TropGeneDB–with 10 ontologies–such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD’s objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach. 2018 2019-02-12T15:16:29Z 2019-02-12T15:16:29Z Journal Article https://hdl.handle.net/10568/99412 en Open Access application/pdf Public Library of Science Venkatesan, A.; Tagny Ngompe, G.; El Hassouni, N.; Chentli, I.; Guignon, V.; Jonquet, C.; Ruiz, M., Larmande, P. (2018) Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PLoS ONE 13(11): e0198270. ISSN: 1932-6203 |
| spellingShingle | ontology agronomy genes information retrieval knowledge organization system computer applications cereal crops Venkatesan, A. Tagny Ngompe, G. El Hassouni, N. Chentli, I. Guignon, Valentin Jonquet, C. Ruíz, M. Larmande, Pierre Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title | Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title_full | Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title_fullStr | Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title_full_unstemmed | Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title_short | Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy |
| title_sort | agronomic linked data agrold a knowledge based system to enable integrative biology in agronomy |
| topic | ontology agronomy genes information retrieval knowledge organization system computer applications cereal crops |
| url | https://hdl.handle.net/10568/99412 |
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