Cottongen

Data Template


Template	gwas	download

Headers


Column	Description
* dataset_name	Name of the GWAS study, the dataset_name should exist in 'dataset_name' column of the 'Dataset' sheet.
* unique_ID	Unique ID.
* genus	Genus of the GWAS.
* species	Species of the GWAS.
group_name	Name of the GWAS group, the GWAS group name should exist in 'group_name' column of the 'GWAS_group' sheet.
group_genus	Genus of the GWAS group (Required if group name is provided).
group_species	Species of the GWAS group (Required if group name is provided).
published_symbol	Published Symbol for the GWAS.
* marker_name	Name of marker found to be assocated with a phenotype.
site_name	It should match 'site_name' in the 'Site' sheet.
gene	Name of the associated gene. Multiple genes, separated by a semicolon or comman (,;), can be added.
trait_ontology_set	Name of the crop trait ontology (entered by the curator who loads the data into the database). If not provided, the site trait ontology will be used.
* trait_name	Phenotype that was found to be associated with marker.
p_value	The p-value of the variant/trait association.
functional_classification	Functional classification.
beta_coefficient	The beta of the variant/trait association
effect	GWAS effect
MAF	Minor Allele Frequency. Not sure how to determine what the minor allele is if paper does not indicate it.
mac	minor_allele_count. used in araGWAS database.
alleles	SNP alleles.
trait_associated_allele	Allele assoicated with the favorable phenotype.
gene_association	Synonymous coding, non-synonymous coding, 3 prime UTR, 5 prime UTR, Intron, Intergenic,etc.
R2	Fraction of the total variation explained by the QTLs.
LOD	The log of the odds ratio
PVE	Phenotypic variance explained.
confidence_interval	Confidence interval of allele-phenotype association.
FDR	.
EMMAX_significance_rank	.
experimental_model	.
statistical_method	.
comments	Any comments on GWAS.
* reference	pub ID of the QTL paper.
##property_name	Special columns (##) : followed by name of the custom property.
MAC

* Required field

cvterms


cv.name	cvterm.name
MAIN	GWAS
MAIN	beta_coefficient
MAIN	comments
MAIN	confidence_interval
MAIN	effect
MAIN	emmax_significance_rank
MAIN	experimental_model
MAIN	fdr
MAIN	functional_classification
MAIN	gene_association
MAIN	lod
MAIN	mac
MAIN	maf
MAIN	p_value
MAIN	panel
MAIN	published_symbol
MAIN	pve
MAIN	r2
MAIN	statistical_method
MAIN	trait_associated_allele
MAIN	unique_key
sequence	allele
sequence	associated_with
sequence	gene
sequence	genetic_marker

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