Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium
Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases)...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/134717 |
| _version_ | 1855520139977424896 |
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| author | Clarke, Jennifer L. Cooper, Laurel D. Poelchau, Monica F. Berardini, Tanya Z. Elser, Justin Farmer, Andrew D. Ficklin, Stephen Kumari, Sunita Laporte, Marie-Angélique Nelson, Rex T. Sadohara, Rie Selby, Peter Thessen, Anne E. Whitehead, Brandon Sen, Taner Z. |
| author_browse | Berardini, Tanya Z. Clarke, Jennifer L. Cooper, Laurel D. Elser, Justin Farmer, Andrew D. Ficklin, Stephen Kumari, Sunita Laporte, Marie-Angélique Nelson, Rex T. Poelchau, Monica F. Sadohara, Rie Selby, Peter Sen, Taner Z. Thessen, Anne E. Whitehead, Brandon |
| author_facet | Clarke, Jennifer L. Cooper, Laurel D. Poelchau, Monica F. Berardini, Tanya Z. Elser, Justin Farmer, Andrew D. Ficklin, Stephen Kumari, Sunita Laporte, Marie-Angélique Nelson, Rex T. Sadohara, Rie Selby, Peter Thessen, Anne E. Whitehead, Brandon Sen, Taner Z. |
| author_sort | Clarke, Jennifer L. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL https://www.agbiodata.org/databases. |
| format | Journal Article |
| id | CGSpace134717 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1347172025-11-11T17:45:28Z Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium Clarke, Jennifer L. Cooper, Laurel D. Poelchau, Monica F. Berardini, Tanya Z. Elser, Justin Farmer, Andrew D. Ficklin, Stephen Kumari, Sunita Laporte, Marie-Angélique Nelson, Rex T. Sadohara, Rie Selby, Peter Thessen, Anne E. Whitehead, Brandon Sen, Taner Z. genomics crops databases phenotypes standard ontologies Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44 databases and resources (https://www.agbiodata.org/databases) covering model or crop plant and animal GGB data, ontologies, pathways, genetic variation and breeding platforms (referred to as 'databases' throughout). One of the goals of the Consortium is to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data management and the integration of datasets which requires data sharing, along with structured vocabularies and/or ontologies. Two AgBioData working groups, focused on Data Sharing and Ontologies, respectively, conducted a Consortium-wide survey to assess the current status and future needs of the members in those areas. A total of 33 researchers responded to the survey, representing 37 databases. Results suggest that data-sharing practices by AgBioData databases are in a fairly healthy state, but it is not clear whether this is true for all metadata and data types across all databases; and that, ontology use has not substantially changed since a similar survey was conducted in 2017. Based on our evaluation of the survey results, we recommend (i) providing training for database personnel in a specific data-sharing techniques, as well as in ontology use; (ii) further study on what metadata is shared, and how well it is shared among databases; (iii) promoting an understanding of data sharing and ontologies in the stakeholder community; (iv) improving data sharing and ontologies for specific phenotypic data types and formats; and (v) lowering specific barriers to data sharing and ontology use, by identifying sustainability solutions, and the identification, promotion, or development of data standards. Combined, these improvements are likely to help AgBioData databases increase development efforts towards improved ontology use, and data sharing via programmatic means. Database URL https://www.agbiodata.org/databases. 2024-03-29 2023-11-24T13:09:05Z 2023-11-24T13:09:05Z Journal Article https://hdl.handle.net/10568/134717 en Open Access application/pdf Oxford University Press Clarke, J.L.; Cooper, L.D.; Poelchau, M.F.; Berardini, T.Z.; Elser, J.; Farmer, A.D.; Ficklin, S.; Kumari, S.; Laporte, M-A.; Nelson, R.T.; Sadohara, R.; Selby, P.; Thessen, A.E.; Whitehead, B.; Sen, T.Z. (2023) Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database 2023: baad076. ISSN: 1758-0463 |
| spellingShingle | genomics crops databases phenotypes standard ontologies Clarke, Jennifer L. Cooper, Laurel D. Poelchau, Monica F. Berardini, Tanya Z. Elser, Justin Farmer, Andrew D. Ficklin, Stephen Kumari, Sunita Laporte, Marie-Angélique Nelson, Rex T. Sadohara, Rie Selby, Peter Thessen, Anne E. Whitehead, Brandon Sen, Taner Z. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title | Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title_full | Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title_fullStr | Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title_full_unstemmed | Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title_short | Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium |
| title_sort | data sharing and ontology use among agricultural genetics genomics and breeding databases and resources of the agbiodata consortium |
| topic | genomics crops databases phenotypes standard ontologies |
| url | https://hdl.handle.net/10568/134717 |
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