Post-composing ontology terms for effcient phenotyping in plant breeding
Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In man...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
2025
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/174021 |
| _version_ | 1855519584830881792 |
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| author | Menda, N. Ellerbrock, B.J. Simoes, C.C. Karaikal, S.K. Nyaga, C. Flores-Gonzalez, M. Tecle, I.Y. Lyon, D. Agbona, A. Agre, A.P. Peteti, P. Akech, V. Asiimwe, A. Fauvelle, E. Meghar, K. Tran, T. Dufour, D. Cooper, L. Laporte, M.A. Arnaud, E. Mueller, L. |
| author_browse | Agbona, A. Agre, A.P. Akech, V. Arnaud, E. Asiimwe, A. Cooper, L. Dufour, D. Ellerbrock, B.J. Fauvelle, E. Flores-Gonzalez, M. Karaikal, S.K. Laporte, M.A. Lyon, D. Meghar, K. Menda, N. Mueller, L. Nyaga, C. Peteti, P. Simoes, C.C. Tecle, I.Y. Tran, T. |
| author_facet | Menda, N. Ellerbrock, B.J. Simoes, C.C. Karaikal, S.K. Nyaga, C. Flores-Gonzalez, M. Tecle, I.Y. Lyon, D. Agbona, A. Agre, A.P. Peteti, P. Akech, V. Asiimwe, A. Fauvelle, E. Meghar, K. Tran, T. Dufour, D. Cooper, L. Laporte, M.A. Arnaud, E. Mueller, L. |
| author_sort | Menda, N. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping. |
| format | Journal Article |
| id | CGSpace174021 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| record_format | dspace |
| spelling | CGSpace1740212025-12-08T09:54:28Z Post-composing ontology terms for effcient phenotyping in plant breeding Menda, N. Ellerbrock, B.J. Simoes, C.C. Karaikal, S.K. Nyaga, C. Flores-Gonzalez, M. Tecle, I.Y. Lyon, D. Agbona, A. Agre, A.P. Peteti, P. Akech, V. Asiimwe, A. Fauvelle, E. Meghar, K. Tran, T. Dufour, D. Cooper, L. Laporte, M.A. Arnaud, E. Mueller, L. ontology plant breeding databases phenotypes data Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping. 2025 2025-04-07T12:53:31Z 2025-04-07T12:53:31Z Journal Article https://hdl.handle.net/10568/174021 en Open Access application/pdf Menda, N., Ellerbrock, B.J., Simoes, C.C., Karaikal, S.K., Nyaga, C., Flores-Gonzalez, M., ... & Mueller, L. (2025). Post-composing ontology terms for efficient phenotyping in plant breeding. Database, 2025, 1-12. |
| spellingShingle | ontology plant breeding databases phenotypes data Menda, N. Ellerbrock, B.J. Simoes, C.C. Karaikal, S.K. Nyaga, C. Flores-Gonzalez, M. Tecle, I.Y. Lyon, D. Agbona, A. Agre, A.P. Peteti, P. Akech, V. Asiimwe, A. Fauvelle, E. Meghar, K. Tran, T. Dufour, D. Cooper, L. Laporte, M.A. Arnaud, E. Mueller, L. Post-composing ontology terms for effcient phenotyping in plant breeding |
| title | Post-composing ontology terms for effcient phenotyping in plant breeding |
| title_full | Post-composing ontology terms for effcient phenotyping in plant breeding |
| title_fullStr | Post-composing ontology terms for effcient phenotyping in plant breeding |
| title_full_unstemmed | Post-composing ontology terms for effcient phenotyping in plant breeding |
| title_short | Post-composing ontology terms for effcient phenotyping in plant breeding |
| title_sort | post composing ontology terms for effcient phenotyping in plant breeding |
| topic | ontology plant breeding databases phenotypes data |
| url | https://hdl.handle.net/10568/174021 |
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