Journal article
Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
Database : the journal of biological databases and curation, Vol.2017
12/09/2017
Handle:
https://hdl.handle.net/2376/116425
PMCID: PMC5727400
PMID: 31725859
Abstract
Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for
Rosaceae
(rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org).
Database URL
:
https://www.citrusgenomedb.org/
,
https://www.coolseasonfoodlegume.org/
,
https://www.cottongen.org/
,
https://www.rosaceae.org/
,
https://www.vaccinium.org/
Metrics
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Details
- Title
- Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
- Creators
- Sook Jung - Department of Horticulture, Washington State University, Pullman, WA, 99164, USATaein Lee - Department of Horticulture, Washington State University, Pullman, WA, 99164, USAChun-Huai Cheng - Department of Horticulture, Washington State University, Pullman, WA, 99164, USAStephen Ficklin - Department of Horticulture, Washington State University, Pullman, WA, 99164, USAJing Yu - Department of Horticulture, Washington State University, Pullman, WA, 99164, USAJodi Humann - Department of Horticulture, Washington State University, Pullman, WA, 99164, USADorrie Main - Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
- Publication Details
- Database : the journal of biological databases and curation, Vol.2017
- Academic Unit
- Horticulture, Department of
- Publisher
- Oxford University Press
- Grant note
- #1444573 / ; ;
- Identifiers
- 99900547787401842
- Language
- English
- Resource Type
- Journal article