CottonGen

General Information

CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. 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.

Homepage https://www.cottongen.org/

Countries that developed this resource United States

Created in 2013

Taxonomic range

Gossypium

Knowledge Domains

Subjects

Awaiting DOI assignment.

Record added: Feb. 28, 2018, 1:01 p.m.
Record updated: July 8, 2019, 5:32 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/bsg-d001056' by 'The FAIRsharing Team' at 17:32, 08 Jul 2019 (approved):

	'onto_disciplines' has been modified:
		Before:
			Agriculture
			Genomics
			Life Sciences
			Plant Genetics
		After:
			Agriculture
			Genomics
			Life Sciences
			Plant Breeding
			Plant Genetics
		Added:
			Plant Breeding
		Removed:

	'onto_domains' has been modified:
		Before:
			Breeding
			Genetic map
			whole genome sequencing assay
		After:
			Genetic map
			whole genome sequencing assay
		Added:
		Removed:
			Breeding

Edits to 'https://fairsharing.org/bsg-d001056' by 'The FAIRsharing Team' at 11:53, 23 Oct 2018 (approved):

	'domains' has been modified:
		Before:
			Agriculture
			Breeding
			Genomics
			Plant Genetics
		After:
			Agriculture
			Breeding
			Genetic map
			Genomics
			Life Science
			Plant Genetics
			Whole genome sequencing
		Added:
			Genetic map
			Life Science
			Whole genome sequencing
		Removed:

In Collections

AgBioData

Tripal

Support

General

contact form	CottonGen Contact Form
online documentation	Data Overview
online documentation	Cotton Trait Ontology
online documentation	About CottonGen
twitter	@CottonGen_news

Tools

BLAST	https://www.cottongen.org/blast
CMap	https://www.cottongen.org/tools/cmap
GBrowse	https://www.cottongen.org/tools/gbrowse
GBrowse_syn	https://www.cottongen.org/tool/gbrowse_syn
JBrowse	https://www.cottongen.org/tools/jbrowse
Sequence Retrieval	https://www.cottongen.org/retrieve/sequences
MapViewer	https://www.cottongen.org/node/6372709

Access / Retrieve Data

Conditions of Use

Data Access

Data Download	https://www.cottongen.org/data/download
Submit Data	https://www.cottongen.org/data/submission
Search QTLs	https://www.cottongen.org/find/qtl
Search Markers	https://www.cottongen.org/search/markers
Search Map	https://www.cottongen.org/find/featuremap/summary
Search Germplasm	https://www.cottongen.org/search/germplasm
Search Genotype	https://www.cottongen.org/find/ssr_genotype
Search Genes and Transcripts	https://www.cottongen.org/find/genes
Search Sequences	https://www.cottongen.org/find/features
Search Traits	https://www.cottongen.org/search/trait

Publications

CottonGen: a genomics, genetics and breeding database for cotton research.

Yu J,Jung S,Cheng CH,Ficklin SP,Lee T,Zheng P,Jones D,Percy RG,Main D
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Funds

Cotton Incorporated (Company)
Southern Association of Agricultural Experiment Station Directors (Consortium)
Dow/Phytogen (Company)
Monsanto (Company)
Bayer Crop Science, Germany (Company)

Maintains

MainLab Bioinformatics, Washington State University, USA (Lab)
United States Department of Agriculture, Agricultural Research Service (USDA-ARS) Crop Germplasm Research Unit, College Station, USA (Government body)
Washington State University, USA (University)

CottonGen

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