Agricultural Sciences in the Big Data Era: Genotype and Phenotype Data Standardization, Utilization and Integration

Deng, C.H.; Naithani, S.; Kumari, S.; Cobo-Simón, I.; Quezada-Rodríguez, E.H.; Skrabisova, M.; Gladman, N.; Correll, M.J.; Sikiru, A.B.; Afuwape, O.O.; et al. Genotype and Phenotype Data Standardization, Utilization and Integration in the Big Data Era for Agricultural Sciences. Database 2023, 2023, doi:10.1093/database/baad088. Deng, C.H.; Naithani, S.; Kumari, S.; Cobo-Simón, I.; Quezada-Rodríguez, E.H.; Skrabisova, M.; Gladman, N.; Correll, M.J.; Sikiru, A.B.; Afuwape, O.O.; et al. Genotype and Phenotype Data Standardization, Utilization and Integration in the Big Data Era for Agricultural Sciences. Database 2023, 2023, doi:10.1093/database/baad088.

Abstract

The Genotype-Phenotype Working Group was established in November 2021 as part of the AgBioData Consortium (https://www.agbiodata.org) with the goal of identifying current challenges in annotating and integrating large-scale genotype and phenotype data. Over the course of the year, the members of this working group identified different types of data sets, explored experimental platforms and methods for data generation, and examined how these data are annotated including the metadata requirements. We conducted a thorough review of publicly funded repositories for raw and processed data for each data type. We also examined several secondary databases and knowledgebases that enable the integration of heterogeneous data types in the context of the Genome Browser, Pathway Networks and tissue-specific gene expression. The review revealed a need for additional infrastructural support, standards, and tools to connect Genotype to Phenotype data and enhance data interoperability for knowledge synthesis and to foster translational research.

Keywords

Genotype; phenotype; sequencing; phenomics; data integration; metadata; standardization

Subject

Biology and Life Sciences, Agricultural Science and Agronomy

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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