CottonGen


26989146	Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. [PMID: 26989146] Jung S, Lee T, Ficklin S, Yu J, Cheng CH, Main D. Abstract The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis tools for Rosaceae crops and Gossypium (cotton). These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform. Chado is highly normalized and uses ontologies to indicate the 'types' of data. Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen. These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic and genotypic data, ontologies and publications. We provide information about how to store these types of data in Chado using GDR and CottonGen as examples sites that were converted from an older legacy infrastructure. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org). © The Author(s) 2016. Published by Oxford University Press. Database (Oxford). 2016:2016() \| 6 Citations (from Europe PMC, 2025-03-15)
24203703	CottonGen: a genomics, genetics and breeding database for cotton research. [PMID: 24203703] Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D. Abstract CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. Nucleic Acids Res. 2014:42(Database issue) \| 155 Citations (from Europe PMC, 2025-03-15)

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. [PMID: 26989146]

Jung S, Lee T, Ficklin S, Yu J, Cheng CH, Main D.

Abstract

The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis tools for Rosaceae crops and Gossypium (cotton). These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform. Chado is highly normalized and uses ontologies to indicate the 'types' of data. Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen. These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic and genotypic data, ontologies and publications. We provide information about how to store these types of data in Chado using GDR and CottonGen as examples sites that were converted from an older legacy infrastructure. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org). © The Author(s) 2016. Published by Oxford University Press.

Database (Oxford). 2016:2016() | 6 Citations (from Europe PMC, 2025-03-15)

CottonGen: a genomics, genetics and breeding database for cotton research. [PMID: 24203703]

Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D.

Abstract

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.

Nucleic Acids Res. 2014:42(Database issue) | 155 Citations (from Europe PMC, 2025-03-15)

URL:	https://www.cottongen.org/
Full name:
Description:	CottonGen is a curated and integrated web-based relational database providing access to publicly available genomic,genetic and breeding data for cotton.
Year founded:	2014
Last update:	2016-10-31
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Plant
Database category:	Gene genome and annotation
Major species:	Gossypium hirsutum
Keywords:	cotton genome

University/Institution:	Washington State University
Address:	Pullman,WA 99164-6414,USA
City:	Pullman
Province/State:	WA
Country/Region:	United States
Contact name (PI/Team):	Dorrie Main
Contact email (PI/Helpdesk):	dorrie@wsu.edu

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Database Commons a catalog of worldwide biological databases