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CC BY V4.0, Open Access
Journal article
Uniform standards for genome databases in forest and fruit trees
Tree genetics & genomes, Vol.8(3), pp.549-557
06/2012
Handle:
https://hdl.handle.net/2376/108411
Abstract
TreeGenes and tree fruit Genome Database Resources serve the international forestry and fruit tree genomics research communities, respectively. These databases hold similar sequence data and provide resources for the submission and recovery of this information in order to enable comparative genomics research. Large-scale genotype and phenotype projects have recently spawned the development of independent tools and interfaces within these repositories to deliver information to both geneticists and breeders. The increase in next generation sequencing projects has increased the amount of data as well as the scale of analysis that can be performed. These two repositories are now working towards a similar goal of archiving the diverse, independent data sets generated from genotype/phenotype experiments. This is achieved through focused development on data input standards (templates), pipelines for the storage and automated curation, and consistent annotation efforts through the application of widely accepted ontologies to improve the extraction and exchange of the data for comparative analysis. Efforts towards standardization are not limited to genotype/phenotype experiments but are also being applied to other data types to improve gene prediction and annotation for de novo sequencing projects. The resources developed towards these goals represent the first large-scale coordinated effort in plant databases to add informatics value to diverse genotype/phenotype experiments.
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Details
- Title
- Uniform standards for genome databases in forest and fruit trees
- Creators
- J Wegrzyn - Department of Plant Sciences University of California at Davis Mail Stop 4 Davis CA 95616 USAD Main - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAB Figueroa - Department of Plant Sciences University of California at Davis Mail Stop 4 Davis CA 95616 USAM Choi - Department of Plant Sciences University of California at Davis Mail Stop 4 Davis CA 95616 USAJ Yu - Department of Plant Sciences University of California at Davis Mail Stop 4 Davis CA 95616 USAD Neale - Department of Plant Sciences University of California at Davis Mail Stop 4 Davis CA 95616 USAS Jung - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAT Lee - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAM Stanton - Clemson University Genomics Institute Clemson University Clemson SC 29634 USAP Zheng - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAS Ficklin - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAI Cho - Department of Computer Science Saginaw Valley State University Saginaw MI 48710 USAC Peace - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAK Evans - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAG Volk - National Center for Genetic Resources Preservation USDA/ARS Fort Collins CO 80521 USAN Oraguzie - Department of Horticulture and Landscape Architecture Washington State University PO Box 646414 Pullman WA 99164 USAC Chen - Citrus Research and Education Center University of Florida Lake Alfred FL 33850 USAM Olmstead - Horticultural Sciences Department–IFAS University of Florida Gainesville FL 32611 USAG Gmitter Jr - Citrus Research and Education Center University of Florida Lake Alfred FL 33850 USAA Abbott - Department of Genetics and Biochemistry Clemson University Clemson SC 29634 USA
- Contributors
- Albert G Abbott (Editor)
- Publication Details
- Tree genetics & genomes, Vol.8(3), pp.549-557
- Academic Unit
- WSU Wenatchee Tree Fruit REC; Department of Horticulture
- Publisher
- Springer-Verlag; Berlin/Heidelberg
- Number of pages
- 9
- Identifiers
- 99900546906301842
- Language
- English
- Resource Type
- Journal article