Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Deng, Cecilia H.; Naithani, Sushma; Kumari, Sunita; Cobo-Simón, Irene; Quezada-Rodríguez, Elsa H.; Skrabisova, Maria; Gladman, Nick; Correll, Melanie J.; Sikiru, Akeem Babatunde; Afuwape, Olusola; Marrano, Annarita; Rebollo, Ines; Zhang, Wentao; Jung, Sook; National Science Foundation (US)

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

17 Pág.

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Main Authors:	Deng, Cecilia H., Naithani, Sushma, Kumari, Sunita, Cobo-Simón, Irene, Quezada-Rodríguez, Elsa H., Skrabisova, Maria, Gladman, Nick, Correll, Melanie J., Sikiru, Akeem Babatunde, Afuwape, Olusola, Marrano, Annarita, Rebollo, Ines, Zhang, Wentao, Jung, Sook
Other Authors:	National Science Foundation (US)
Format:	artículo biblioteca
Language:	English
Published:	Oxford University Press 2023-12-11
Online Access:	http://hdl.handle.net/10261/349435 http://dx.doi.org/10.13039/100000001 http://dx.doi.org/10.13039/100005825 https://api.elsevier.com/content/abstract/scopus_id/85179640905
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spelling	dig-inia-es-10261-3494352024-05-18T20:41:39Z Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences Deng, Cecilia H. Naithani, Sushma Kumari, Sunita Cobo-Simón, Irene Quezada-Rodríguez, Elsa H. Skrabisova, Maria Gladman, Nick Correll, Melanie J. Sikiru, Akeem Babatunde Afuwape, Olusola Marrano, Annarita Rebollo, Ines Zhang, Wentao Jung, Sook National Science Foundation (US) National Institute of Food and Agriculture (US) Deng, Cecilia H. [0000-0002-2954-762X] Naithani, Sushma [0000-0001-7819-4552] Kumari, Sunita [0000-0001-9166-1450] Cobo-Simón, Irene [0000-0002-7648-7471] Quezada-Rodríguez, Elsa H. [0000-0001-7789-4987] Skrabisova, Maria [0000-0003-2879-1062] Gladman, Nick [0000-0002-9000-8377] Correll, Melanie J. [0000-0002-2432-6107] Sikiru, Akeem Babatunde [0000-0003-4956-7094] Marrano, Annarita [0000-0001-9560-2706] Rebollo, Ines [0000-0002-9899-0801] Jung, Sook [0000-0003-3968-2769] 17 Pág. Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org. We acknowledge the funding to AgBioData Consortium through the National Science Foundation (16) for the Research Coordination Network (RCN) project (award abstract #2126334), USDA National Institute of Food and Agriculture Specialty Crop Research Initiative project [2022-51181-38449], and USDA National Institute of Food and Agriculture National Research Support Project 10. Peer reviewed 2024-03-06T12:11:23Z 2024-03-06T12:11:23Z 2023-12-11 artículo http://purl.org/coar/resource_type/c_6501 Database Magazine 2023: baad088 (2023) http://hdl.handle.net/10261/349435 10.1093/database/baad088 1758-0463 http://dx.doi.org/10.13039/100000001 http://dx.doi.org/10.13039/100005825 38079567 2-s2.0-85179640905 https://api.elsevier.com/content/abstract/scopus_id/85179640905 en Instituto de Ciencias Forestales (ICIFOR) Publisher's version https://doi.org/10.1093/database/baad088 Sí open application/pdf Oxford University Press
institution	INIA ES
collection	DSpace
country	España
countrycode	ES
component	Bibliográfico
access	En linea
databasecode	dig-inia-es
tag	biblioteca
region	Europa del Sur
libraryname	Biblioteca del INIA España
language	English
description	17 Pág.
author2	National Science Foundation (US)
author_facet	National Science Foundation (US) Deng, Cecilia H. Naithani, Sushma Kumari, Sunita Cobo-Simón, Irene Quezada-Rodríguez, Elsa H. Skrabisova, Maria Gladman, Nick Correll, Melanie J. Sikiru, Akeem Babatunde Afuwape, Olusola Marrano, Annarita Rebollo, Ines Zhang, Wentao Jung, Sook
format	artículo
author	Deng, Cecilia H. Naithani, Sushma Kumari, Sunita Cobo-Simón, Irene Quezada-Rodríguez, Elsa H. Skrabisova, Maria Gladman, Nick Correll, Melanie J. Sikiru, Akeem Babatunde Afuwape, Olusola Marrano, Annarita Rebollo, Ines Zhang, Wentao Jung, Sook
spellingShingle	Deng, Cecilia H. Naithani, Sushma Kumari, Sunita Cobo-Simón, Irene Quezada-Rodríguez, Elsa H. Skrabisova, Maria Gladman, Nick Correll, Melanie J. Sikiru, Akeem Babatunde Afuwape, Olusola Marrano, Annarita Rebollo, Ines Zhang, Wentao Jung, Sook Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
author_sort	Deng, Cecilia H.
title	Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
title_short	Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
title_full	Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
title_fullStr	Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
title_full_unstemmed	Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
title_sort	genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences
publisher	Oxford University Press
publishDate	2023-12-11
url	http://hdl.handle.net/10261/349435 http://dx.doi.org/10.13039/100000001 http://dx.doi.org/10.13039/100005825 https://api.elsevier.com/content/abstract/scopus_id/85179640905
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Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

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