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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #345300

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: The art of curation at a biological database: principles and application

Author
item Odell, Sarah - University Of California, Davis
item Lazo, Gerard
item Woodhouse, Margaret - Orise Fellow
item Hane, David - Eg Consulting (SELF-EMPLOYED)
item Sen, Taner

Submitted to: Current Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2017
Publication Date: 12/2/2017
Citation: Odell, S.G., Lazo, G.R., Woodhouse, M.R., Hane, D.L., Sen, T.Z. 2017. The art of curation at a biological database: principles and application. Current Plant Biology. 11-12:2-11. https://doi.org/10.1016/j.cpb.2017.11.001.
DOI: https://doi.org/10.1016/j.cpb.2017.11.001

Interpretive Summary: The variety and quantity of data being produced by biological research has grown dramatically in recent years, resulting in an expansion of our understanding of biological systems. However, this abundance of data has brought up new challenges, especially in curation. The role of biocurators is in part to filter research outcomes as they are generated, not only so that information is formatted and consolidated into locations that can provide long-term data sustainability, but also to ensure that the relevant data that was captured is reliable, reusable, and accessible. At GrainGenes, a long-term stably-funded centralized repository for small grains data, curators have implemented a workflow for locating, parsing, and uploading new data so that the most important, peer-reviewed, high-quality research is available to users as quickly as possible with rich links to past research outcomes. In many ways, biocuration lies somewhere between an art and a science. With the emerging presence of reference genomes for the small-grain crops, it is paramount to build foundation databases to build upon. In this work we provide the principles and practical considerations that we follow at GrainGenes, the international repository for small grains data, including for wheat, barley, rye, and oat. Three case studies of GrainGenes curated data are provided to demonstrate how our work allows users, i.e., small grains geneticists and breeders, to harness high-quality small grains data to develop plants with enhanced agronomic traits.

Technical Abstract: The variety and quantity of data being produced by biological research has grown dramatically in recent years, resulting in an expansion of our understanding of biological systems. However, this abundance of data has brought new challenges, especially in curation. The role of biocurators is in part to filter research outcomes as they are generated, not only so that information is formatted and consolidated into locations that can provide long-term data sustainability, but also to ensure that the relevant data that was captured is reliable, reusable, and accessible. In many ways, biocuration lies somewhere between an art and a science. At GrainGenes, a long-time, stably-funded centralized repository for data about wheat, barley, oat, rye and other small grains, curators have implemented a workflow for locating, parsing, and uploading new data so that the most important, peer-reviewed, high-quality research is available to users as quickly as possible with rich links to past research outcomes. In this report, we illustrate the principles and practical considerations of curation that we follow at GrainGenes with three case studies for curating a gene, a QTL, and genomic elements. These examples demonstrate how our work allows users, i.e., small grains geneticists and breeders, to harness high-quality small grains data at GrainGenes to help them develop plants with enhanced agronomic traits.