Crop ontology: integration of standard variables
The Crop Ontology (CO, http://www.cropontology.org/) is a resource of the Integrated Breeding Platform (IBP, http://integratedbreeding.net/) providing breeders with crop specific terms for fieldbook edition and data annotation. Until Mai 2015, a plant phenotype was annotated with 3 CO identifiers fo...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Conference Paper |
| Lenguaje: | Inglés |
| Publicado: |
2016
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/78758 |
| _version_ | 1855528172349554688 |
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| author | Valette, L. Pietragalla, J. Laporte, Marie-Angélique Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, Alberto F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, Antonio José Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville-Hamilton, N. Ruaraidh Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R. |
| author_browse | Afolabi, A. Arnaud, Elizabeth Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, Alberto F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. Laporte, Marie-Angélique López Montes, Antonio José Menda, N. Nelson, R. Ofodile, S. Patil, S. Pietragalla, J. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Reinhard Simon, Guvener Selim Sackville-Hamilton, N. Ruaraidh Shrestha, R. Teme, N. Valette, L. Weltzien, Eva |
| author_facet | Valette, L. Pietragalla, J. Laporte, Marie-Angélique Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, Alberto F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, Antonio José Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville-Hamilton, N. Ruaraidh Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R. |
| author_sort | Valette, L. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The Crop Ontology (CO, http://www.cropontology.org/) is a resource of the Integrated Breeding Platform (IBP, http://integratedbreeding.net/) providing breeders with crop specific terms for fieldbook edition and data annotation. Until Mai 2015, a plant phenotype was annotated with 3 CO identifiers for the trait, the method and the scale, respectively. Yet, breeders’ fieldbook and most phenotypic databases are designed to annotate a datapoint with only one identifier. To meet the need of providing one single identifier to an observation variable, the CO and IBP teams have worked on integrating the notion of variable into the CO. This has led to a thorough revision of the structure of the Trait Dictionary (TD) template. The TD template is a user-friendly xls file that is used to submit terms to CO which are then stored in the IBP Breeding Management System and other information systems (NextGen, Agtrials…).
The most notable changes to the TD template are the addition of the term type “variable” and the decomposition of a trait into an entity and an attribute so as to formalize the trait definition and to foster the mapping with external ontologies (TO, PO, PATO, CHEBI, EO, PDO, GO…). Guidelines document how to post-compose variables.
Along with the partners, the CO and IBP team have been working on formatting and curating the TD of pigeonpea (ICRISAT), cowpea (IITA), wheat (CIMMYT), groundnut (ICRISAT/USDA), yam (IITA), chickpea (ICRISAT), lentil (ICARDA), cassava (IITA), soybean (IITA/USDA), common bean (CIAT), rice (IRRI), pearl millet (ICRISAT), sorghum (CIRAD/ICRISAT), and maize (CIMMYT). |
| format | Conference Paper |
| id | CGSpace78758 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| record_format | dspace |
| spelling | CGSpace787582025-01-27T15:00:52Z Crop ontology: integration of standard variables Valette, L. Pietragalla, J. Laporte, Marie-Angélique Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, Alberto F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, Antonio José Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville-Hamilton, N. Ruaraidh Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R. ontology standards data information systems plant breeding The Crop Ontology (CO, http://www.cropontology.org/) is a resource of the Integrated Breeding Platform (IBP, http://integratedbreeding.net/) providing breeders with crop specific terms for fieldbook edition and data annotation. Until Mai 2015, a plant phenotype was annotated with 3 CO identifiers for the trait, the method and the scale, respectively. Yet, breeders’ fieldbook and most phenotypic databases are designed to annotate a datapoint with only one identifier. To meet the need of providing one single identifier to an observation variable, the CO and IBP teams have worked on integrating the notion of variable into the CO. This has led to a thorough revision of the structure of the Trait Dictionary (TD) template. The TD template is a user-friendly xls file that is used to submit terms to CO which are then stored in the IBP Breeding Management System and other information systems (NextGen, Agtrials…). The most notable changes to the TD template are the addition of the term type “variable” and the decomposition of a trait into an entity and an attribute so as to formalize the trait definition and to foster the mapping with external ontologies (TO, PO, PATO, CHEBI, EO, PDO, GO…). Guidelines document how to post-compose variables. Along with the partners, the CO and IBP team have been working on formatting and curating the TD of pigeonpea (ICRISAT), cowpea (IITA), wheat (CIMMYT), groundnut (ICRISAT/USDA), yam (IITA), chickpea (ICRISAT), lentil (ICARDA), cassava (IITA), soybean (IITA/USDA), common bean (CIAT), rice (IRRI), pearl millet (ICRISAT), sorghum (CIRAD/ICRISAT), and maize (CIMMYT). 2016 2017-01-13T15:23:48Z 2017-01-13T15:23:48Z Conference Paper https://hdl.handle.net/10568/78758 en Open Access Valette, L.; Pietragalla, J.; Laporte, M-A.; Afolabi, A.; Boukar, O.; Cannon, S.B.; Diers, D.W.; Dreher, K.A.; Gaur, P.M.; Guerrero, A.F.; Hash, C.T.; Hualla, V.; Inoussa, D.; Kalberer, S.R.; Kondombo-Barro, C.; Kumar, S.; Lopez-Montes, A.; Menda, N.; Nelson, R.; Ofodile, S.; Patil, S.; Prasad, P.; Rajendran, K.; Rami, J-F.; Rathore, A.; Sackville Hamilton, N.R.; Reinhard, S.; Teme, N.; Weltzien-Rattunde, E.; Arnaud, E.; Shrestha, R. (2016) Crop ontology: integration of standard variables. [Abstract] presented at XXIV Plant and Animal Genome Conference. San Diego, CA (USA) 9-13 Jan 2016. |
| spellingShingle | ontology standards data information systems plant breeding Valette, L. Pietragalla, J. Laporte, Marie-Angélique Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, Alberto F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, Antonio José Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville-Hamilton, N. Ruaraidh Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R. Crop ontology: integration of standard variables |
| title | Crop ontology: integration of standard variables |
| title_full | Crop ontology: integration of standard variables |
| title_fullStr | Crop ontology: integration of standard variables |
| title_full_unstemmed | Crop ontology: integration of standard variables |
| title_short | Crop ontology: integration of standard variables |
| title_sort | crop ontology integration of standard variables |
| topic | ontology standards data information systems plant breeding |
| url | https://hdl.handle.net/10568/78758 |
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