Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology
Abstract The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 pa...
| Autores principales: | , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Oxford University Press
2024
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| Acceso en línea: | https://hdl.handle.net/10568/135574 |
| _version_ | 1855540488869773312 |
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| author | Cooper, Laurel D. Elser, Justin Laporte, Marie-Angelique Arnaud, Elizabeth Jaiswal, Pankaj |
| author_browse | Arnaud, Elizabeth Cooper, Laurel D. Elser, Justin Jaiswal, Pankaj Laporte, Marie-Angelique |
| author_facet | Cooper, Laurel D. Elser, Justin Laporte, Marie-Angelique Arnaud, Elizabeth Jaiswal, Pankaj |
| author_sort | Cooper, Laurel D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Abstract The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology. |
| format | Journal Article |
| id | CGSpace135574 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1355742025-11-11T19:07:07Z Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology Cooper, Laurel D. Elser, Justin Laporte, Marie-Angelique Arnaud, Elizabeth Jaiswal, Pankaj genomics crops breeding ontologies Abstract The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology. 2024-01-05 2023-12-19T10:44:01Z 2023-12-19T10:44:01Z Journal Article https://hdl.handle.net/10568/135574 en Open Access application/pdf Oxford University Press Cooper, L.; Elser, J.; Laporte, M.; Arnaud, E.; Jaiswal, P. (2023) Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology. Nucleic Acids Research gkad1028. ISSN: 0305-1048 |
| spellingShingle | genomics crops breeding ontologies Cooper, Laurel D. Elser, Justin Laporte, Marie-Angelique Arnaud, Elizabeth Jaiswal, Pankaj Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title | Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title_full | Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title_fullStr | Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title_full_unstemmed | Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title_short | Planteome 2024 Update: Reference ontologies and knowledgebase for plant biology |
| title_sort | planteome 2024 update reference ontologies and knowledgebase for plant biology |
| topic | genomics crops breeding ontologies |
| url | https://hdl.handle.net/10568/135574 |
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